Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/CHEBI_89983 LPS core http://purl.obolibrary.org/obo/CHEBI_18154 polysaccharide Core oligosaccharide A short chain of sugar residues within a lipopolysaccharide, containing an oligosaccharide component which attaches directly to a lipid A component. {External definition} http://purl.obolibrary.org/obo/OAE_0000363 infection AE http://purl.obolibrary.org/obo/OAE_0000001 adverse event infectious adverse event An adverse event that has an outcome of a pathogen infection, i.e., an infection caused by a pathogen such as a virus, bacterium, or parasite. http://purl.obolibrary.org/obo/OAE_0000488 bacterial infection AE http://purl.obolibrary.org/obo/OAE_0000363 infection AE bacterial infection AE An infection AE that results in detrimental colonization of a host organism by bacteria http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. http://purl.obolibrary.org/obo/OBI_0000576 scattered molecular aggregate http://purl.obolibrary.org/obo/BFO_0000027 object aggregate Collective A material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum 'nominal measurement datum' A measurement datum that is reported on a categorical scale. http://purl.obolibrary.org/obo/OBI_0001486 disposition to be bound by an MHC protein complex http://purl.obolibrary.org/obo/BFO_0000016 disposition MHC ligand disposition Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex. http://purl.obolibrary.org/obo/OBI_1110045 disposition to be bound by an adaptive immune receptor http://purl.obolibrary.org/obo/BFO_0000016 disposition epitope disposition Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. http://purl.obolibrary.org/obo/OBI_1110132 CD8 receptor http://purl.obolibrary.org/obo/PR_000000001 protein CD8 A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. http://purl.obolibrary.org/obo/OAE_0000001 adverse event http://purl.obolibrary.org/obo/OGMS_0000061 pathological bodily process adverse reaction; AE A pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event. http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex antibody An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component. http://purl.obolibrary.org/obo/IDO_0000436 infectious disease http://purl.obolibrary.org/obo/OGMS_0000031 disease tranmissible disease Disease whose physical basis is an infectious disorder. http://purl.obolibrary.org/obo/IDO_0000438 invasion disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Invasion factor; invasin Disposition borne by a biological macromolecule that is the disposition to facilitate breach of and entry through host barriers. http://purl.obolibrary.org/obo/IDO_0000481 infectious disease incidence proportion http://purl.obolibrary.org/obo/BFO_0000019 quality cumulative incidence of infectious disease Site occupied by an organism population lacking any infectious disease incidences. http://purl.obolibrary.org/obo/IDO_0000482 infection incidence proportion http://purl.obolibrary.org/obo/BFO_0000019 quality cumulative incidence of infection Quality that inheres in an organism population and is the proportion of members of the population not infected at the beginning of a specified period of time who become infected during the specified period of time. http://purl.obolibrary.org/obo/IDO_0000498 active immunization against pathogen http://purl.obolibrary.org/obo/IDO_0000497 immunization against pathogen inoculation Immunization that begins with exposure of an organism to antigen and results in immunity against a pathogen http://purl.obolibrary.org/obo/IDO_0000514 susceptible population http://purl.obolibrary.org/obo/IDO_0000509 organism population at-risk population Organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. http://purl.obolibrary.org/obo/IDO_0000515 normal resident microbiota population http://purl.obolibrary.org/obo/IDO_0000509 organism population normal resident microflora population Organism population whose members are participating in non-parasitic symbiosis with a particular host. http://purl.obolibrary.org/obo/IDO_0000562 antibiotic http://purl.obolibrary.org/obo/BFO_0000040 material entity antibacterial Material entity that is used to treat bacterial infections and which bears either a bactericidal disposition or a bacteriostatic disposition. http://purl.obolibrary.org/obo/IDO_0000651 primary immunodeficiency http://purl.obolibrary.org/obo/IDO_0000617 immunodeficiency congenital immunodeficiency Immunodeficiency that exists in an organism because of a genetic predisposition. http://purl.obolibrary.org/obo/TRANS_0000005 vector-borne pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000002 indirect pathogen transmission process Indirect pathogen transmission process during which the pathogen is indirectly transferred from a reservoir, source or host via an animate intermediary vector to another host. http://purl.obolibrary.org/obo/IDO_0001009 pathogen birth process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary that marks the start of the life cycle of a pathogen. http://purl.obolibrary.org/obo/IDO_0001011 drug-based immunosuppressed organism http://purl.obolibrary.org/obo/IDO_0001005 pathologically immunosuppressed organism Pathologically immunosuppressed organism that is experiencing drug-based immunosuppression. http://purl.obolibrary.org/obo/TRANS_0000028 propagative pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000015 biologic pathogen transmission process Biological pathogen transmission process during which the pathogen that is ingested with the blood meal undergoes simple multiplication in the body of the vector. http://purl.obolibrary.org/obo/IDO_0001344 infection start process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary that marks the start of an infection, latency process, and incubation process. http://purl.obolibrary.org/obo/CHEBI_18059 lipid http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids. http://purl.obolibrary.org/obo/CHEBI_52206 biochemical role http://purl.obolibrary.org/obo/CHEBI_24432 biological role A biological role played by the molecular entity or part thereof within a biochemical context. http://purl.obolibrary.org/obo/CHEBI_6495 lipoprotein http://purl.obolibrary.org/obo/CHEBI_33837 conjugated protein A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids. http://purl.obolibrary.org/obo/CHEBI_65212 polysaccharide derivative http://purl.obolibrary.org/obo/CHEBI_63299 carbohydrate derivative A carbohydrate derivative that is any derivative of a polysaccharide. http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc. http://purl.obolibrary.org/obo/CHEBI_24397 glycophospholipid http://purl.obolibrary.org/obo/CHEBI_16247 phospholipid Any phospholipid that contain both phosphate and carbohydrate as integral structural components. http://purl.obolibrary.org/obo/CHEBI_33563 glycolipid http://purl.obolibrary.org/obo/CHEBI_35740 liposaccharide Any member of class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide). Some substances classified as bacterial glycolipids have the sugar part acylated by one or more fatty acids and the glycerol part may be absent. http://purl.obolibrary.org/obo/CHEBI_61082 lipid-linked peptidoglycan http://purl.obolibrary.org/obo/CHEBI_8005 peptidoglycan A peptidoglycan with a phosphate linkage to a lipid. http://purl.obolibrary.org/obo/CHEBI_8005 peptidoglycan http://purl.obolibrary.org/obo/CHEBI_86469 peptidoglycosaminoglycan A peptidoglycosaminoglycan formed by alternating residues of beta-(1->4)-linked N-acetylglucosamine and N-acetylmuramic acid {2-amino-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose} residues. Attached to the carboxy group of the muramic acid is a peptide chain of three to five amino acids. http://purl.obolibrary.org/obo/CHEBI_73170 bacterial virulence gene B http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity A bacterial gene that can produce a gene product that is at least partially responsible for enabling a bacterium to be pathogenic http://purl.obolibrary.org/obo/CHEBI_86469 peptidoglycosaminoglycan http://purl.obolibrary.org/obo/CHEBI_18085 glycosaminoglycan A family of glycosaminoglycan formed by alternating residues of D-glucosamine and either muramic acid {2-amino-3-O-[(S)-1-carboxyethyl]-2-deoxy-D-glucose} or L-talosaminuronic acid (2-amino-2-deoxy-L-taluronic acid), which are usually N-acetylated or N-glycoloylated. Those containing muramic acid residues are known as peptidoglycans while those containing L-talosaminuronic acid residues are known as pseudopeptidoglycans. The carboxyl group of the muramic acid is commonly substituted by a peptide containing residues of both L- and D-amino acids, whereas that of L-talosaminuronic acid is substituted by a peptide consisting of L-amino acids only. http://purl.obolibrary.org/obo/CLO_0009823 microbial survival inside cell line cell http://purl.obolibrary.org/obo/GO_0008150 biological process A biological process that presents the survival of a microbe inside a cell line cell. http://purl.obolibrary.org/obo/CLO_0009824 bacterial survival inside cell line cell http://purl.obolibrary.org/obo/CLO_0009823 microbial survival inside cell line cell A microbial survival inside cell line cell where the microbe is a bacterium. http://purl.obolibrary.org/obo/UO_0000210 colony forming unit http://purl.obolibrary.org/obo/UO_0000189 count unit A dimensionless count unit which is a measure of viable bacterial numbers. http://purl.obolibrary.org/obo/APOLLO_SV_00000075 infectious disease control objective specification http://purl.obolibrary.org/obo/IAO_0000005 objective specification Objective specification that is realized by processes that are able or likely to stop the spread of a disease in a population. http://purl.obolibrary.org/obo/APOLLO_SV_00000174 disease transmission model http://purl.obolibrary.org/obo/IAO_0000064 algorithm Algorithm that models the progress of a transmissible disease in a population. http://purl.obolibrary.org/obo/APOLLO_SV_00000229 place closure control strategy http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Infectious disease control strategy that has an action specification that is realized in closing facilities where organisms congregate during times when the facilities normally would be open. http://purl.obolibrary.org/obo/APOLLO_SV_00000230 case isolation control strategy http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Infectious disease control strategy that has an action specification that is realized in isolating organsims who are infectious. http://purl.obolibrary.org/obo/APOLLO_SV_00000308 vector control strategy http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Infectious disease control strategy that has a vector control action specification as part. http://purl.obolibrary.org/obo/APOLLO_SV_00000327 quarantine control strategy http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Infectious disease control strategy whereby asymptomatic carriers who have had contact with pathogens are prevented from having contact with other susceptible organisms. http://purl.obolibrary.org/obo/APOLLO_SV_00000489 contact isolation control measure http://purl.obolibrary.org/obo/APOLLO_SV_00000230 case isolation control strategy A case isolation control measure that has an action specification that is realized in preventing one or more infectious organisms from having physical contact with other organisms. http://purl.obolibrary.org/obo/APOLLO_SV_00000541 disease surveillance objective specification http://purl.obolibrary.org/obo/IAO_0000005 objective specification Objective specification whose endpoint is human awareness of the level of a disease in a particular population of a given biological taxon during some time interval. http://www.ontologyrepository.com/CommonCoreOntologies/DescriptiveInformationContentEntity descriptive information content entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information Content Entity that consists of a set of propositions that describe some Entity. http://purl.obolibrary.org/obo/OGMS_0000129 physical sign http://purl.obolibrary.org/obo/BFO_0000040 material entity An abnormal material entity that is part of a patient and hypothesized to be clinically relevant. http://purl.obolibrary.org/obo/OGMS_0000141 processual sign http://purl.obolibrary.org/obo/BFO_0000015 process An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant. http://purl.obolibrary.org/obo/OGMS_0000142 qualitative sign http://purl.obolibrary.org/obo/BFO_0000019 quality An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant. http://purl.obolibrary.org/obo/IDO_0001040 bacteriostatic http://purl.obolibrary.org/obo/IDO_0001090 static agent Static agent bearing a bacteriostatic disposition. http://purl.obolibrary.org/obo/IDO_0001029 parasiticidal disposition http://purl.obolibrary.org/obo/IDO_0001092 cidal agent disposition Disposition inhering in a material entity, that is realized in a process of killing parasites. http://purl.obolibrary.org/obo/PATO_0000051 morphology http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure. http://purl.obolibrary.org/obo/PATO_0000052 shape http://purl.obolibrary.org/obo/PATO_0000051 morphology A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc). http://purl.obolibrary.org/obo/PATO_0000404 coiled http://purl.obolibrary.org/obo/PATO_0000052 shape A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals). http://purl.obolibrary.org/obo/PATO_0000406 curved http://purl.obolibrary.org/obo/PATO_0000052 shape A curvature quality inhering in a bearer by virtue of the bearer's having or being marked by a curve or smoothly rounded bend. http://purl.obolibrary.org/obo/PATO_0001154 elongated http://purl.obolibrary.org/obo/PATO_0000052 shape A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width. http://purl.obolibrary.org/obo/PATO_0001241 physical object quality http://purl.obolibrary.org/obo/BFO_0000019 quality A quality which inheres in a continuant. http://purl.obolibrary.org/obo/PATO_0001356 pleomorphic http://purl.obolibrary.org/obo/PATO_0000052 shape A shape quality inhering in a cell by virtue of the bearer's ability to take on two or more different shapes during its life cycle. http://purl.obolibrary.org/obo/PATO_0001455 aerobic http://purl.obolibrary.org/obo/PATO_0001995 organismal quality A quality inhering in a bearer by virtue of the bearer's dependence on oxygen. http://purl.obolibrary.org/obo/PATO_0001456 anaerobic http://purl.obolibrary.org/obo/PATO_0001995 organismal quality A quality inhering in a bearer by virtue of the bearer's independence on oxygen. http://purl.obolibrary.org/obo/PATO_0001499 spherical http://purl.obolibrary.org/obo/PATO_0000052 shape A spheroid quality inhering in a bearer by virtue of the bearer's resembling a ball (a sphere whose equatorial diameter is equal to the polar diameter). http://purl.obolibrary.org/obo/PATO_0001544 flexible http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. http://purl.obolibrary.org/obo/PATO_0001545 inflexible http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. http://purl.obolibrary.org/obo/PATO_0001873 cylindrical http://purl.obolibrary.org/obo/PATO_0000052 shape A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section. http://purl.obolibrary.org/obo/PATO_0001891 ovate http://purl.obolibrary.org/obo/PATO_0000052 shape A spheroid quality inhering in a bearer by virtue of the bearer's exhibiting a continuous convex surface with an axis of symmetry and one axis longer than the other; egg-shaped. http://purl.obolibrary.org/obo/GO_0062039 biofilm matrix http://purl.obolibrary.org/obo/GO_0031012 extracellular matrix A structure lying external to microbial cells. A biofilm is an aggregate of surface-associated cells, and the biofilm matrix is the envelope of polymeric substances that surrounds the cells. http://purl.obolibrary.org/obo/IDO_0001090 static agent http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity with a static agent disposition. http://purl.obolibrary.org/obo/IDO_0001356 communicability start process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the start of a communicability interval. http://purl.obolibrary.org/obo/BIDO_0000601 bacterial infectious disorder http://purl.obolibrary.org/obo/IDO_0000504 infectious disorder Infectious disorder that has some bacterium as part, that exists as a result of a process of formation of disorder initiated by the bacterium. http://purl.obolibrary.org/obo/BIDO_0000602 bacterial infectious disease http://purl.obolibrary.org/obo/IDO_0000436 infectious disease Infectious disease that has its material basis in some bacterial infectious disorder. http://purl.obolibrary.org/obo/BIDO_0000773 bacteria aggregate http://purl.obolibrary.org/obo/BFO_0000027 object aggregate Object aggregate whose members are bacteria. http://purl.obolibrary.org/obo/BIDO_0000779 bacterial pathogenesis http://purl.obolibrary.org/obo/GO_0009405 pathogenesis Pathogenesis process realization of a pathogenic disposition inhering in some bacterium or bacteria population, having at least the proper process parts: (1) toxin biosynthetic process, and (2) appearance of disorder. http://purl.obolibrary.org/obo/BIDO_0000782 bacterial infectious disease epidemic http://purl.obolibrary.org/obo/IDO_0000502 infectious disease epidemic Process of bacterial infectious disease realizations for which there is a statistically significant increase in the bacterial infectious disease incidence of a population. http://purl.obolibrary.org/obo/BIDO_0000783 bacterial infectious disease pandemic http://purl.obolibrary.org/obo/IDO_0000503 infectious disease pandemic Process in which multiple bacterial infectious disease epidemics of the same type of bacterial infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. http://purl.obolibrary.org/obo/BIDO_0000784 bacteria birth process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary that marks the beginning of the lify cycle of a bacterium. http://purl.obolibrary.org/obo/BIDO_0000785 bacteria death process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary that marks the end of the life cycle of some bacterium. http://purl.obolibrary.org/obo/BIDO_0000786 bacterium incubation process http://purl.obolibrary.org/obo/IDO_0001384 incubation process Incubation process of some bacterium beginning with infection by the bacterium and ending with the manifestation of symptoms. http://purl.obolibrary.org/obo/BIDO_0000787 bacterial latency process http://purl.obolibrary.org/obo/IDO_0001385 latency process Latency process involving a bacterium, during which the bacterium lies dormant within the host, and ending when the bacterium starts to reproduce. http://purl.obolibrary.org/obo/BIDO_0000802 bacterial toxin disorder http://purl.obolibrary.org/obo/OGMS_0000045 disorder Disorder the formation of which involves some bacterial toxin. http://purl.obolibrary.org/obo/IDO_0001112 generative stage http://purl.obolibrary.org/obo/BFO_0000015 process Temporal subdivision of a developmental process. http://purl.obolibrary.org/obo/IDO_0001298 outer mucus layer http://purl.obolibrary.org/obo/GO_0070701 mucus layer The outer of two mucus layers secreted by epithelial cells in the colon; the outer mucus layer is loosely packed and can be colonized by bacteria. [database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394] http://purl.obolibrary.org/obo/IDO_0001379 infectious disease surveillance objective specification http://purl.obolibrary.org/obo/IAO_0000005 objective specification Objective specification whose endpoint is human awareness of the level of an infectious disease in a particular population of a given biological taxon during some time interval. http://purl.obolibrary.org/obo/IDO_0001380 human infectious disposition http://purl.obolibrary.org/obo/ido.owl/IDO_0001157 infectious disposition Infectious disposition that is the disposition to become part of a disorder in a host of the species Homo Sapiens. http://purl.obolibrary.org/obo/IDO_0001381 pathogen developmental process http://purl.obolibrary.org/obo/GO_0032502 developmental process Developmental process whose specific outcome is the progression of a pathogen. http://purl.obolibrary.org/obo/IDO_0001382 infectious agent developmental process http://purl.obolibrary.org/obo/IDO_0001381 pathogen developmental process Developmental process whose specific outcome is the progression of an infectious agent. http://purl.obolibrary.org/obo/IDO_0001383 infectious structure developmental process http://purl.obolibrary.org/obo/IDO_0001381 pathogen developmental process Developmental process whose specific outcome is the progression of an infectious structure. http://purl.obolibrary.org/obo/IDO_0001384 incubation process http://purl.obolibrary.org/obo/BFO_0000015 process Process beginning with the establishing of an infection in a host and ending with the onset of symptoms by the host, during which pathogens are multiplying in the host. http://purl.obolibrary.org/obo/IDO_0001385 latency process http://purl.obolibrary.org/obo/BFO_0000015 process Process beginning with the establishing of an infection in a host and ending when the host becomes contagious, during which pathogens are multiplying in the host. http://purl.obolibrary.org/obo/IDO_0001386 infectious disease incidence profile http://purl.obolibrary.org/obo/BFO_0000144 process profile Process profile comprised of a series of determinate infectious disease incidence qualities caused by a specific pathogen in a population over time. http://purl.obolibrary.org/obo/IDO_0001388 Infectious disease proportion profile http://purl.obolibrary.org/obo/BFO_0000144 process profile Process profile comprised of a series of infectious disease incidence proportion qualities caused by a specific pathogen per unit time. http://purl.obolibrary.org/obo/IDO_0001389 infection prevalence process profile http://purl.obolibrary.org/obo/BFO_0000144 process profile Process profile comprised of a series of determinate infection prevalence qualities in a population over time. http://purl.obolibrary.org/obo/IDO_0001390 infectious disease prevalence process profile http://purl.obolibrary.org/obo/BFO_0000144 process profile Process profile comprised of a series of determinate infectious disease prevalence qualities in a population over time. http://purl.obolibrary.org/obo/IDO_0001391 infectious disease holoendemicity http://purl.obolibrary.org/obo/IDO_0000490 infectious disease endemicity Infectious disease endemicity that inheres in an organism population in virtue of the fact that intra-population transmission occurs with an extremely high frequency, where most of population's older members are asymptomatic carriers due to adaptive immunity, whereas its younger members are more likely to be symptomatic carriers. http://purl.obolibrary.org/obo/http://purl.obolibrary.org/obo/GO_0015627 type II protein secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex. [database_cross_reference: PMID:16448494] http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000001 entity An entity that has temporal parts and that happens, unfolds or develops through time. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) http://purl.obolibrary.org/obo/BFO_0000023 role http://purl.obolibrary.org/obo/BFO_0000017 realizable entity A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant Continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. http://purl.obolibrary.org/obo/BFO_0000035 process boundary http://purl.obolibrary.org/obo/BFO_0000003 occurrent p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/BFO_0000015 process b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) http://purl.obolibrary.org/obo/IAO_0000003 measurement unit label http://purl.obolibrary.org/obo/IAO_0000009 datum label A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. http://purl.obolibrary.org/obo/IAO_0000005 objective specification http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity directive information content entity Directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. http://purl.obolibrary.org/obo/IAO_0000007 action specification http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity directive information content entity Directive information entity that describes an action the bearer will take http://purl.obolibrary.org/obo/IAO_0000009 datum label http://purl.obolibrary.org/obo/IAO_0000030 information content entity A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification Plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity directive information content entity Directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/IAO_0000027 data item A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000015 process Process that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000066 investigation http://purl.obolibrary.org/obo/OBI_0000011 planned process a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). http://purl.obolibrary.org/obo/OBI_0000070 assay http://purl.obolibrary.org/obo/OBI_0000011 planned process Planned process with the objective to produce information about some evaluant. http://purl.obolibrary.org/obo/OBI_0000086 reagent role http://purl.obolibrary.org/obo/BFO_0000023 role Role inhering in a molecular entity when the molecular entity is used to produce a chemical reaction to detect, measure, or produce other substances. http://purl.obolibrary.org/obo/OBI_0000094 material processing http://purl.obolibrary.org/obo/OBI_0000011 planned process Planned process which results in physical changes in a specified input material. http://purl.obolibrary.org/obo/OBI_0000237 antigen role http://purl.obolibrary.org/obo/CHEBI_24432 biological role Biological role inhering in some molecular entity, that stimulates an immune response when identified by the immune systems cells. http://purl.obolibrary.org/obo/OBI_0001503 MHC protein complex binding to ligand http://purl.obolibrary.org/obo/OBI_0001588 binding The process in which a ligand binds to an MHC molecule to form a stable complex http://purl.obolibrary.org/obo/OBI_0001511 disposition to be a product of antigen processing and presentation http://purl.obolibrary.org/obo/BFO_0000016 disposition A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell. http://purl.obolibrary.org/obo/OBI_0001588 binding http://purl.obolibrary.org/obo/GO_0008150 biological process The process of material entities forming complexes. http://purl.obolibrary.org/obo/OBI_0001702 immunoglobulin binding to epitope http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR). http://purl.obolibrary.org/obo/OBI_0001720 B cell epitope specific immune complex formation http://purl.obolibrary.org/obo/GO_0097281 immune complex formation immune complex formation resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000030 object Object that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor http://purl.obolibrary.org/obo/GO_0008150 biological process is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding. http://purl.obolibrary.org/obo/OBI_1110022 adaptive immune receptor http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex Receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. http://purl.obolibrary.org/obo/OBI_1110023 immunogen http://purl.obolibrary.org/obo/OBI_1110034 antigen An antigen bearing the immunogen role. http://purl.obolibrary.org/obo/OBI_1110034 antigen http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Molecular entity bearing an antigen role. http://purl.obolibrary.org/obo/OBI_1110057 MHC:epitope complex binding to TCR http://purl.obolibrary.org/obo/OBI_1110014 epitope binding by adaptive immune receptor a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule. http://purl.obolibrary.org/obo/OBI_1110082 immunogen role http://purl.obolibrary.org/obo/CHEBI_24432 biological role Biological role inhering in some molecular entity, that is capable on its own of eliciting an immune response when identified by the immune system cells. http://purl.obolibrary.org/obo/OBI_1110086 restricting MHC role http://purl.obolibrary.org/obo/BFO_0000023 role The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. http://purl.obolibrary.org/obo/OGMS_0000031 disease http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://purl.obolibrary.org/obo/OGMS_0000063 disease course http://purl.obolibrary.org/obo/BFO_0000015 process Totality of all processes through which a given disease instance is realized. http://purl.obolibrary.org/obo/OGMS_0000090 treatment http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process http://purl.obolibrary.org/obo/PATO_0001995 organismal quality http://purl.obolibrary.org/obo/PATO_0001241 physical object quality A quality that inheres in an entire organism or part of an organism. http://purl.obolibrary.org/obo/PR_000000001 protein http://purl.obolibrary.org/obo/CHEBI_16670 peptide An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. http://purl.obolibrary.org/obo/PR_000001004 CD4 molecule http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence. http://purl.obolibrary.org/obo/UO_0000051 concentration unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. http://purl.obolibrary.org/obo/UO_0000212 colony forming unit per volume http://purl.obolibrary.org/obo/UO_0000051 concentration unit A concentration unit which a measure of viable bacterial numbers in a given volume. http://purl.obolibrary.org/obo/VO_0000001 vaccine http://purl.obolibrary.org/obo/OBI_0000047 processed material A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine. http://purl.obolibrary.org/obo/DRON_00000001 clinical drug role http://purl.obolibrary.org/obo/BFO_0000023 role The role of a material entity to prevent, diagnose, treat, or study disease and/or its effects http://purl.obolibrary.org/obo/OGMS_0000097 health care encounter http://purl.obolibrary.org/obo/OGMS_0000096 health care process A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter http://purl.obolibrary.org/obo/GO_0110001 toxin-antitoxin complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A bacterial protein complex that neutralises its own toxin by complexing the toxin with the antitoxin. The antitoxin can be either a protein or an RNA. The neutralising toxin-antitoxin complex also acts as a transcriptional repressor of the toxin-antitoxin operon. http://purl.obolibrary.org/obo/OHMI_0000005 bacterial microbiome http://purl.obolibrary.org/obo/OHMI_0000003 microbiome A microbiome that includes a collective population of bacterial organisms. http://purl.obolibrary.org/obo/APOLLO_SV_00000550 contact tracing http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Infectious disease control strategy that identifies and treats contacted organisms in a host population. http://purl.obolibrary.org/obo/GO_0120100 bacterial-type flagellum motor http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A transmembrane complex embedded in the cytoplasmic membrane which is the motor force, or torque, generator of the bacterial-type flagellum. The motor consists of a membrane-anchored rotor complex surrounded by one or more stator complexes in the cytoplasmic membrane. The stator consists of a hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. Examples are the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species. The rotor complex consists of a membrane-anchored ring and the motor switch complex, which controls the direction of flagellar rotation. http://purl.obolibrary.org/obo/IDO_0001109 infectious agent generative stage http://purl.obolibrary.org/obo/IDO_0001111 pathogen generative stage Pathogen generative stage that is a temporal subdivision of an infectious agent developmental process. http://purl.obolibrary.org/obo/IDO_0001355 incubation start process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the start of an incubation interval. http://purl.obolibrary.org/obo/CHEBI_16247 phospholipid http://purl.obolibrary.org/obo/CHEBI_18059 lipid A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides. http://purl.obolibrary.org/obo/CHEBI_16646 carbohydrate http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid Nucleic acid composed of nucleotides containing deoxyribose and linked by phosphodiester bonds. http://purl.obolibrary.org/obo/CHEBI_18085 glycosaminoglycan http://purl.obolibrary.org/obo/CHEBI_22506 aminoglycan Any polysaccharide containing a substantial proportion of aminomonosaccharide residues. http://purl.obolibrary.org/obo/CHEBI_18154 polysaccharide http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule A biomacromolecule consisting of large numbers of monosaccharide residues linked glycosidically. This term is commonly used only for those containing more than ten monosaccharide residues. http://purl.obolibrary.org/obo/CHEBI_30049 teichoic acid http://purl.obolibrary.org/obo/CHEBI_65212 polysaccharide derivative Bacterial polysaccharide derivatives of glycerol phosphate or ribitol phosphate linked via phosphodiester bonds, whose main function is to fortify the cell wall. In some parasites, they serve as a site of attachment to mucosal membranes. http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule Macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases. http://purl.obolibrary.org/obo/CHEBI_47040 lipid A http://purl.obolibrary.org/obo/CHEBI_25051 lipid As The glycolipid moiety of bacterial lipopolysaccharide (R can be either hydrogen or a fatty acyl group). http://purl.obolibrary.org/obo/CHEBI_50699 oligosaccharide http://purl.obolibrary.org/obo/CHEBI_16646 carbohydrate A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. http://purl.obolibrary.org/obo/CHEBI_63299 carbohydrate derivative http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity Any organooxygen compound derived from a carbohydrate by replacement of one or more hydroxy group(s) by an amino group, a thiol group or similar heteroatomic groups. The term also includes derivatives of these compounds. http://purl.obolibrary.org/obo/CL_0000000 cell http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity This should be an inferred subclass of BFO:object. -John http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/CL_0000000 cell A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment). http://purl.obolibrary.org/obo/CL_0000084 T cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. http://purl.obolibrary.org/obo/CL_0000094 granulocyte http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A leukocyte with abundant granules in the cytoplasm. http://purl.obolibrary.org/obo/CL_0000096 mature neutrophil http://purl.obolibrary.org/obo/CL_0000775 neutrophil A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive. http://purl.obolibrary.org/obo/CL_0000097 mast cell http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. http://purl.obolibrary.org/obo/CL_0000234 phagocyte http://purl.obolibrary.org/obo/CL_0000219 motile cell Any cell capable of ingesting particulate matter via phagocytosis. http://purl.obolibrary.org/obo/CL_0000235 macrophage http://purl.obolibrary.org/obo/CL_0000234 phagocyte A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. http://purl.obolibrary.org/obo/CL_0000236 B cell http://purl.obolibrary.org/obo/CL_0000945 lymphocyte of B lineage A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity. http://purl.obolibrary.org/obo/CL_0000451 dendretic cell http://purl.obolibrary.org/obo/CL_0000738 leukocyte A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). http://purl.obolibrary.org/obo/CL_0000542 lymphocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin. http://purl.obolibrary.org/obo/CL_0000563 endospore http://purl.obolibrary.org/obo/CL_0000520 prokaryotic cell A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged. [database_cross_reference: GOC:tfm][database_cross_reference: ISBN:0618947256] http://purl.obolibrary.org/obo/CL_0000576 monocyte http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. http://purl.obolibrary.org/obo/CL_0000583 alveolar macrophage http://purl.obolibrary.org/obo/CL_0000235 macrophage A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. http://purl.obolibrary.org/obo/CL_0000623 natural killer cell http://purl.obolibrary.org/obo/CL_0001067 group 1 innate lymphoid cell A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. http://purl.obolibrary.org/obo/CL_0000738 leukocyte http://purl.obolibrary.org/obo/CL_0000219 motile cell An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. http://purl.obolibrary.org/obo/CL_0000766 myeloid leukocyte http://purl.obolibrary.org/obo/CL_0000738 leukocyte A cell of the monocyte, granulocyte, or mast cell lineage. http://purl.obolibrary.org/obo/CL_0000775 neutrophil http://purl.obolibrary.org/obo/CL_0000094 granulocyte Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. http://purl.obolibrary.org/obo/CL_0000776 immature neutrophil http://purl.obolibrary.org/obo/CL_0000775 neutrophil Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking. http://purl.obolibrary.org/obo/CL_0000785 mature B cell http://purl.obolibrary.org/obo/CL_0000236 B cell A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen. http://purl.obolibrary.org/obo/CL_0000786 plasma cell http://purl.obolibrary.org/obo/CL_0000946 antibody secreting cell A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. http://purl.obolibrary.org/obo/CL_0000787 memory B cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative. http://purl.obolibrary.org/obo/CL_0000813 memory T cell http://purl.obolibrary.org/obo/CL_0002419 mature T cell A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure. http://purl.obolibrary.org/obo/CL_0000911 effector T cell http://purl.obolibrary.org/obo/CL_0002419 mature T cell A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. http://purl.obolibrary.org/obo/CL_0000945 lymphocyte of B lineage http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A lymphocyte of B lineage with the commitment to express an immunoglobulin complex. http://purl.obolibrary.org/obo/CL_0000947 IgE plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell A long lived plasma cell that secretes IgE. http://purl.obolibrary.org/obo/CL_0000951 IgE short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell A short lived plasma cell that secretes IgE. http://purl.obolibrary.org/obo/CL_0000968 Be cell http://purl.obolibrary.org/obo/CL_0000785 mature B cell A mature B cell that produces cytokines that can influence CD4 T cell differentiation. http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell http://purl.obolibrary.org/obo/CL_0000786 plasma cell A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow. http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell http://purl.obolibrary.org/obo/CL_0000786 plasma cell A fully differentiated plasma cell that lives for months. http://purl.obolibrary.org/obo/CL_0000976 IgA short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. http://purl.obolibrary.org/obo/CL_0000977 IgG short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell A short lived plasma cell that secretes IgG. http://purl.obolibrary.org/obo/CL_0000978 IgM short lived plasma cell http://purl.obolibrary.org/obo/CL_0000975 short lived plasma cell A short lived plasma cell that secretes IgM. http://purl.obolibrary.org/obo/CL_0000985 IgG plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell A fully differentiated plasma cell that secretes IgG. http://purl.obolibrary.org/obo/CL_0000986 IgM plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell A fully differentiated plasma cell that secretes IgM. http://purl.obolibrary.org/obo/CL_0000987 IgA plasma cell http://purl.obolibrary.org/obo/CL_0000974 long lived plasma cell A fully differentiated plasma cell that secretes IgA. http://purl.obolibrary.org/obo/CL_0002419 mature T cell http://purl.obolibrary.org/obo/CL_0000084 T cell A T cell that expresses a T cell receptor complex and has completed T cell selection. http://purl.obolibrary.org/obo/UBERON_0000178 blood http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity A fluid that is composed of blood plasma and erythrocytes. http://purl.obolibrary.org/obo/UBERON_0000467 anatomical system http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. http://purl.obolibrary.org/obo/UBERON_0002405 immune system http://purl.obolibrary.org/obo/UBERON_0000467 anatomical system Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. http://purl.obolibrary.org/obo/IDO_0100533 infectious disease endemic site http://purl.obolibrary.org/obo/BFO_0000029 site Site occupied by an organism population bearing an infectious disease endemicity. http://purl.obolibrary.org/obo/IDO_0100535 infectious disease free site http://purl.obolibrary.org/obo/BFO_0000029 site Site occupied by an organism population lacking any infectious disease incidences. http://purl.obolibrary.org/obo/IDO_0100537 infectious disease non-endemic site http://purl.obolibrary.org/obo/BFO_0000029 site Site occupied by an organism population lacking infectious disease endemicity. http://purl.obolibrary.org/obo/IDO_0100722 infectious disease surveillance http://purl.obolibrary.org/obo/OBI_0000011 planned process Planned process that is the realization of an infectious disease surveillance objective specification. http://purl.obolibrary.org/obo/IDO_0001028 bacteriostatic disposition http://purl.obolibrary.org/obo/IDO_0001091 static agent disposition Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of bacteria. http://purl.obolibrary.org/obo/IDO_0001387 infectious disease incidence rate profile http://purl.obolibrary.org/obo/BFO_0000144 process profile Process profile comprised of a series of infectious disease rate qualities caused by a specific pathogen per unit time. http://purl.obolibrary.org/obo/IDO_0001083 pathogen birth temporal region http://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region Zero-dimensional temporal region occupied by a pathogen birth process boundary. http://purl.obolibrary.org/obo/IDO_0001091 static agent disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of bacteria, fungi, or parasites, or inhibiting the replication of viruses. http://purl.obolibrary.org/obo/IDO_0001092 cidal agent disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition inhering in a material entity, that is realized in a process of killing bacteria, fungi, parasites, or viruses. http://purl.obolibrary.org/obo/IDO_0001348 infection start temporal region http://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region Zero-dimensional temporal region occupied by an infection start process boundary. http://purl.obolibrary.org/obo/ido.owl/CARO_0000005 anatomical space http://purl.obolibrary.org/obo/BFO_0000029 site Site generated by morphogenetic or physiologic processes that is bounded by an anatomical surface. http://purl.obolibrary.org/obo/ido.owl/CARO_0000062 cell space http://purl.obolibrary.org/obo/ido.owl/CARO_0000005 anatomical space Anatomical space that is part of a cell. http://purl.obolibrary.org/obo/ido.owl/IDO_0001026 fungistatic disposition http://purl.obolibrary.org/obo/IDO_0001091 static agent disposition Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of fungi. http://purl.obolibrary.org/obo/ido.owl/IDO_0001036 pathogen portal of entry site http://purl.obolibrary.org/obo/ido.owl/CARO_0000005 anatomical space Anatomical space through which a pathogen enters an organism. http://purl.obolibrary.org/obo/ido.owl/IDO_0001037 pathogen portal of exit site http://purl.obolibrary.org/obo/ido.owl/CARO_0000005 anatomical space Anatomical space through which a pathogen exits an organism. http://purl.obolibrary.org/obo/ido.owl/IDO_0001107 source of infection site http://purl.obolibrary.org/obo/ido.owl/CARO_0000005 anatomical space Anatomical space in which an infection appears in a host organism. http://purl.obolibrary.org/obo/ido.owl/IDO_0001130 pathogen vector role http://purl.obolibrary.org/obo/IDO_0001096 pathogen transporter role A pathogen transporter role that is borne by an organism active in the transfer of an infectious agent or infectious structure to an organism of another species in which it can realize its infectious disposition. http://www.ontologyrepository.com/CommonCoreOntologies/Country country http://www.ontologyrepository.com/CommonCoreOntologies/GeopoliticalEntity geopolitical entity A Geopolitical Entity that delimits a Government with effective internal and external sovereignty over the region and its population, and which is not dependent on or subject to any other power or Geopolitical Entity. http://www.ontologyrepository.com/CommonCoreOntologies/DirectiveInformationContentEntity directive information content entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information Content Entity that consists of a set of propositions or images (as in the case of a blueprint) that prescribe some Entity. http://www.ontologyrepository.com/CommonCoreOntologies/DivisionOfGeopoliticalEntity division of geopolitical entity http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion geospatial region A Geospatial Region that is a fiat division of a Geopolitical Entity and not a Geopolitical Entity. http://www.ontologyrepository.com/CommonCoreOntologies/GeopoliticalEntity geopolitical entity http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion geospatial region A geospatial region that delimits the authority of a formally constituted government to exercise its control within the bounded area. http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialLocation geospatial location http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion geospatial region A Geospatial Region at which an Entity or Event is located. http://www.ontologyrepository.com/CommonCoreOntologies/GeospatialRegion geospatial region http://purl.obolibrary.org/obo/BFO_0000029 site A site at or near the surface of the Earth. http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc. http://purl.obolibrary.org/obo/CHEBI_25212 metabolite http://purl.obolibrary.org/obo/CHEBI_52206 biochemical role Any intermediate or product resulting from metabolism. The term 'metabolite' subsumes the classes commonly known as primary and secondary metabolites. http://purl.obolibrary.org/obo/CHEBI_50860 organic molecular entity http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Any molecular entity that contains carbon. http://purl.obolibrary.org/obo/CHEBI_76969 bacterial metabolite http://purl.obolibrary.org/obo/CHEBI_75787 prokaryotic metabolite http://purl.obolibrary.org/obo/chebi.owl http://purl.obolibrary.org/obo/CHEBI_16412 lipopolysaccharide http://purl.obolibrary.org/obo/CHEBI_35740 liposaccharide Liposaccharide natural compounds consisting of a trisaccharide repeating unit (two heptose units and octulosonic acid) with oligosaccharide side chains and 3-hydroxytetradecanoic acid units (they are a major constituent of the cell walls of Gram-negative bacteria). http://purl.obolibrary.org/obo/CHEBI_33837 conjugated protein http://purl.obolibrary.org/obo/PR_000000001 protein Conjugated protein is a protein that contains a non-peptide component, usually in stoichiometric proportion. http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Molecular entity of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. http://purl.obolibrary.org/obo/CHEBI_64637 O-polysaccharide http://purl.obolibrary.org/obo/CHEBI_65212 polysaccharide derivative A repetitive glycan polysaccharide contained within a lipopolysaccharide (LPS). The O-antigen is attached to the core oligosaccharide, and comprises the outermost domain of the LPS molecule. http://purl.obolibrary.org/obo/CHEBI_72813 exopolysaccharide http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule A biomacromolecule composed of carbohydrate residues which is secreted by a microorganism into the surrounding environment. http://purl.obolibrary.org/obo/CHEBI_25051 lipid As http://purl.obolibrary.org/obo/CHEBI_24397 glycophospholipid Glycophospholipids that are the components of endotoxins held responsible for the toxicity of Gram-negative bacteria. Lipid A is the innermost of the three regions of the lipopolysaccharide (LPS) molecule, and its hydrophobic nature allows it to anchor the LPS to the outer membrane. Four acyl chains attached directly to two (1->6)-linked glucosamine sugars are beta-hydroxy acyl chains usually between 10 and 16 carbons in length. Two additional acyl chains are often attached to the beta-hydroxy group. http://purl.obolibrary.org/obo/CHEBI_33694 biomacromolecule http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule A macromolecule formed by a living organism. http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acid http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid Nucleic acid composed of nucleotides containing ribose and linked by phosphodiester bonds. http://purl.obolibrary.org/obo/CHEBI_48081 bacteriocin http://purl.obolibrary.org/obo/CHEBI_25903 peptide antibiotic Polypeptides synthesized by specific strains of bacteria that are lethal against other strains of the same or related species. http://purl.obolibrary.org/obo/GO_0005215 transporter activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells. http://purl.obolibrary.org/obo/GO_0005575 cellular_component http://purl.obolibrary.org/obo/BFO_0000040 material entity A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome). http://purl.obolibrary.org/obo/GO_0005576 extracellular region http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite. http://purl.obolibrary.org/obo/GO_0005618 cell wall http://purl.obolibrary.org/obo/GO_0030312 external encapsulating structure The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins. http://purl.obolibrary.org/obo/GO_0005856 cytoskeleton http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles. [database_cross_reference: GOC:mah][database_cross_reference: ISBN:0198547684][database_cross_reference: PMID:16959967] http://purl.obolibrary.org/obo/GO_0006113 fermentation http://purl.obolibrary.org/obo/GO_0009987 cellular process The anaerobic enzymatic conversion of organic compounds, especially carbohydrates, coupling the oxidation and reduction of NAD/H and the generation of adenosine triphosphate (ATP). http://purl.obolibrary.org/obo/GO_0006261 DNA-dependent DNA replication http://purl.obolibrary.org/obo/GO_0006260 DNA replication A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands. http://purl.obolibrary.org/obo/GO_0006810 transport http://purl.obolibrary.org/obo/GO_0051234 establishment of localization The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein. http://purl.obolibrary.org/obo/GO_0007114 cell budding http://purl.obolibrary.org/obo/GO_0051301 cell division A form of asexual reproduction, occurring in certain bacteria and fungi (e.g. yeasts) and some primitive animals in which an individual arises from a daughter cell formed by pinching off a part of the parent cell. The budlike outgrowths so formed may sometimes remain attached to the parent cell. http://purl.obolibrary.org/obo/GO_0008152 metabolic process http://purl.obolibrary.org/obo/GO_0008150 biological process The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation. http://purl.obolibrary.org/obo/GO_0009060 aerobic respiration http://purl.obolibrary.org/obo/GO_0045333 cellular respiration The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which requires oxygen as the terminal electron acceptor. http://purl.obolibrary.org/obo/GO_0015031 protein transport http://purl.obolibrary.org/obo/GO_0015833 peptide transport The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/GO_0016020 membrane http://purl.obolibrary.org/obo/GO_0005575 cellular_component A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it. http://purl.obolibrary.org/obo/GO_0016043 cellular component organization http://purl.obolibrary.org/obo/GO_0071840 cellular component organization or biogenesis A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component. [ GOC:jl GOC:ai GOC:mah ] http://purl.obolibrary.org/obo/GO_0016192 vesicle-mediated transport http://purl.obolibrary.org/obo/GO_0009987 cellular process A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane. http://purl.obolibrary.org/obo/GO_0022610 biological adhesion http://purl.obolibrary.org/obo/GO_0008150 biological process The attachment of a cell, organism or acellular structure to a substrate, another cell, organism or acellular structure. http://purl.obolibrary.org/obo/GO_0022829 wide pore channel activity http://purl.obolibrary.org/obo/GO_0015267 channel activity Enables the transport of a solute across a membrane via a large pore, un-gated channel. Examples include gap junctions, which transport substances from one cell to another; and porins which transport substances in and out of bacteria, mitochondria and chloroplasts. http://purl.obolibrary.org/obo/GO_0022857 transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0005215 transporter activity Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. http://purl.obolibrary.org/obo/GO_0030312 external encapsulating structure http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space. http://purl.obolibrary.org/obo/GO_0031012 extracellular matrix http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues. http://purl.obolibrary.org/obo/GO_0032505 reproduction of a single-celled organism http://purl.obolibrary.org/obo/GO_0000003 reproduction The biological process in which new individuals are produced by one or two single-celled organisms. The new individuals inherit some proportion of their genetic material from the parent or parents. [database_cross_reference: GOC:isa_complete] http://purl.obolibrary.org/obo/GO_0034645 cellular macromolecule biosynthetic process http://purl.obolibrary.org/obo/GO_0044260 cellular macromolecule metabolic process The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, carried out by individual cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process http://purl.obolibrary.org/obo/GO_0071704 organic substance metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0044260 cellular macromolecule metabolic process http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass, as carried out by individual cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0048500 signal recognition particle http://purl.obolibrary.org/obo/GO_1990904 ribonucleoprotein complex A complex of protein and RNA which facilitates translocation of proteins across membranes. [database_cross_reference: GOC:mlg] http://purl.obolibrary.org/obo/GO_0051234 establishment of localization http://purl.obolibrary.org/obo/GO_0008150 biological process Process that localizes a substance or cellular component via movement, tethering or selective degradation. http://purl.obolibrary.org/obo/GO_0065003 protein-containing complex assembly http://purl.obolibrary.org/obo/GO_0022607 cellular component assembly The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0071704 organic substance metabolic process http://purl.obolibrary.org/obo/GO_0008152 metabolic process The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0090304 nucleic acid metabolic process http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process Any cellular metabolic process involving nucleic acids. [database_cross_reference: GOC:dph][database_cross_reference: GOC:tb] http://purl.obolibrary.org/obo/GO_0046225 bacteriocin catabolic process http://purl.obolibrary.org/obo/GO_0009407 toxin catabolic process The chemical reactions and pathways resulting in the breakdown of a bacteriocin, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/GO_0046819 protein secretion by the type V secretion system http://purl.obolibrary.org/obo/GO_0098776 protein transport across the cell outer membrane The process in which proteins mediate their own secretion across the outer membrane through a beta-barrel pore structure formed by the C-terminal domain of the protein precursor. Following passage across the outer membrane, the mature protein is released from the pore by an autocatalytic activity. Proteins secreted by the Type V system are first translocated across the plasma membrane by the Sec pathway. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0046868 mesosome http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity An intracellular, often complex, membranous structure, sometimes with additional membranous lamellae inside, found in bacteria. They are associated with synthesis of DNA and secretion of proteins. http://purl.obolibrary.org/obo/GO_0051104 DNA-dependent DNA replication DNA ligation http://purl.obolibrary.org/obo/GO_0006266 DNA ligation The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase, that contributes to DNA-dependent DNA replication. http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.obolibrary.org/obo/BFO_0000015 process Process that modulates a measurable attribute of any biological process, quality or function. http://purl.obolibrary.org/obo/GO_0090729 toxin activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Interacting selectively with one or more biological molecules in another (target) organism, initiating pathogenesis (leading to an abnormal, generally detrimental state) in the target organism. The activity should refer to an evolved function of the active gene product, i.e. one that was selected for. Examples include the activity of botulinum toxin, and snake venom. http://purl.obolibrary.org/obo/UBERON_0000463 organism substance http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://purl.obolibrary.org/obo/UBERON_0016482 dental plaque http://purl.obolibrary.org/obo/ENVO_00002034 biofilm A soft, thin film of food debris, mucin, and dead epithelial cells deposited on the teeth, providing the medium for the growth of various bacteria. The main inorganic components are calcium and phosphorus, with small amounts of magnesium, potassium, and sodium; the organic matrix consists of polysaccharides, proteins, carbohydrates, lipids, and other components. Plaque plays an important etiologic role in the development of dental caries and periodontal and gingival diseases and provides the base for the development of materia alba; calcified plaque forms dental calculus. http://purl.obolibrary.org/obo/PR_000025848 type I interferon http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that consists solely of an Interferon alpha/beta domain (Pfam:PF00143) and which binds to a specific cell surface receptor complex known as the IFN-alpha receptor (IFNAR), a heterodimer of IFNAR1 and IFNAR2 chains. http://purl.obolibrary.org/obo/PR_000036195 bacterial protein http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is encoded in the genome of some Bacteria . http://purl.obolibrary.org/obo/CMO_0001109 disease severity measurement http://purl.obolibrary.org/obo/OBI_0000938 categorical measurement datum Any measurement of the degree to which the presentation of a disease state has caused pain or damage, established one or more lesions or infectious colonies, and/or taken over or interfered with the normal functioning of the body as a whole, or of one or more organs, tissues, cells or subcellular mechanisms of an organism. http://purl.obolibrary.org/obo/CMO_0002653 bacterial infection severity score http://purl.obolibrary.org/obo/CMO_0002652 bacterial infection severity measurement A measurement of bacterial infection severity which is derived from a combination of multiple measurements and/or an objective or subjective ranking or rating system according to a specified formula or set of criteria. http://purl.obolibrary.org/obo/CMO_0002654 bacterial infection severity score based on mucosal leukocyte infiltration http://purl.obolibrary.org/obo/CMO_0002653 bacterial infection severity score A ranking or rating of bacterial infection severity which is based on or derived from the ratio of the number of leukocytes in a sample of mucosal membrane to total number of cells the that sample. http://purl.obolibrary.org/obo/CMO_0002655 bacterial infection severity score based on inflammatory foci in exudate http://purl.obolibrary.org/obo/CMO_0002653 bacterial infection severity score A ranking or rating of bacterial infection severity which is based on or derived from the number and/or size of foci of inflammatory cells (that is, leukocytes, especially neutrophils, macrophages, monocytes, eosinophils, and/or basophils) in a sample of exudate from an infected tissue or organ. An exudate is a fluid with a high content of protein and cellular debris which has escaped from blood vessels and has been deposited in tissues or on tissue surfaces, usually as a result of inflammation. http://purl.obolibrary.org/obo/CMO_0002656 bacteria count http://purl.obolibrary.org/obo/CMO_0002652 bacterial infection severity measurement The enumeration, i.e. measurement of the total number, of bacteria in a specified sample of an infected tissue or bodily fluid, or in the entire body of the host. http://purl.obolibrary.org/obo/CMO_0002657 total number of bacterial colony forming units recovered http://purl.obolibrary.org/obo/CMO_0002656 bacteria count The enumeration, i.e. measurement of the total number, of bacterial colony forming units (CFUs) in a specified sample of fluid removed from and/or solution used to wash the interior of a cavity in a body or an organ. A bacterial CFU is an individual bacterium which is able to clonally propagate itself into an entire colony of identical cells. http://purl.obolibrary.org/obo/CMO_0002658 logarithm of the total number of bacterial colony forming units recovered http://purl.obolibrary.org/obo/CMO_0002657 total number of bacterial colony forming units recovered The logarithm of the enumeration, i.e. measurement of the total number, of bacterial colony forming units (CFUs) in a specified sample of fluid removed from and/or solution used to wash the interior of a cavity in a body or an organ. A logarithm is the power to which a base, such as 10, must be raised to produce a given number. A bacterial CFU is an individual bacterium which is able to clonally propagate itself into an entire colony of identical cells. http://purl.obolibrary.org/obo/DRON_00000028 active ingredient http://purl.obolibrary.org/obo/DRON_00000030 role of scattered molecular aggregate A role of a scattered molecular aggregate that is part of a drug product that is realized by (1) administration of the drug to an organism followed by (2) some change in the structure or functioning of some part of the organism http://purl.obolibrary.org/obo/OGMS_0000061 pathological bodily process http://purl.obolibrary.org/obo/OGMS_0000060 bodily process A bodily process that is clinically abnormal. http://purl.obolibrary.org/obo/UO_0000000 unit http://purl.obolibrary.org/obo/IAO_0000030 information content entity "A unit of measurement is a standardized quantity of a physical quality." [Wikipedia:Wikipedia] http://snomed.info/sct/22642004 Bacterial bacteriophage typing http://purl.obolibrary.org/obo/OBI_0000070 assay An assay for detecting bacteria by subjecting them to strain-specific bacteriophages. http://purl.obolibrary.org/obo/GENEPIO_0000033 fecal indicator bacteria count http://purl.obolibrary.org/obo/STATO_0000047 count Number of indicator micro-organisms (colony forming units) present in a sample that have been used to suggest the presence of pathogens. http://purl.obolibrary.org/obo/GENEPIO_0000043 bacteria density http://purl.obolibrary.org/obo/GENEPIO_0001626 environmental datum Number of bacteria in sample http://purl.obolibrary.org/obo/GEO_000000370 geographical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity that is (1) a bona fide or fiat object part of the crust, any bodies of liquid on or contained within the crust, or planetary boundary layer (if present) of a terrestrial planet (including Earth), dwarf planet, exoplanet, natural satellite, planetesimal, or small Solar System body, and that (2) overlaps the planetary surface (including having a boundary that coincides with part of the planetary surface). http://purl.obolibrary.org/obo/GEO_000000372 geographical region http://purl.obolibrary.org/obo/GEO_000000370 geographical entity Geographical entity that is demarcated at least in part by one or more closed fiat boundaries all of whose lines are part of the planetary surface. http://purl.obolibrary.org/obo/IDO_0000445 resistance to drug http://purl.obolibrary.org/obo/IDO_0000444 protective resistance Protective resistance that mitigates the damaging effects of a drug. http://purl.obolibrary.org/obo/IDO_0000502 infectious disease epidemic http://purl.obolibrary.org/obo/BFO_0000015 process Process of infectious disease realizations for which there is a statistically significant increase in the infectious disease incidence of a population. http://purl.obolibrary.org/obo/IDO_0000509 organism population http://purl.obolibrary.org/obo/BFO_0000027 object aggregate Aggregate of organisms of the same species. http://purl.obolibrary.org/obo/IDO_0000581 antibiotic resistance http://purl.obolibrary.org/obo/IDO_0000445 resistance to drug Resistance to drug that mitigates the damaging effects of an antibiotic. http://purl.obolibrary.org/obo/IDO_0000629 host role http://purl.obolibrary.org/obo/BFO_0000023 role Role borne by an acellular structure containing a distinct material entity, or organism whose extended organism contains a distinct material entity, realized in use of that structure or organism as a site of reproduction or replication. http://purl.obolibrary.org/obo/OGMS_0000087 extended organism http://purl.obolibrary.org/obo/BFO_0000027 object aggregate Object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. http://purl.obolibrary.org/obo/STATO_0000047 count http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A count is a data item denoted by an integer and represented the number of instances or occurences of an entity http://purl.obolibrary.org/obo/TRANS_0000000 pathogen transmission process http://purl.obolibrary.org/obo/BFO_0000015 process Process in which a pathogen is transmitted directly or indirectly to a new host. http://purl.obolibrary.org/obo/TRANS_0000002 indirect pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000000 pathogen transmission process Pathogen transmission process in which a pathogen is indirectly transferred to a host by intermediary vehicles or vectors. http://purl.obolibrary.org/obo/TRANS_0000007 contact pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000000 pathogen transmission process Pathogen transmission process in which a pathogen is transferred to a host through surface-to-surface contact. http://purl.obolibrary.org/obo/TRANS_0000008 droplet pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000002 indirect pathogen transmission process Indirect pathogen transmission process in which a pathogen is transmitted from a host expelling respiratory droplets to another host. http://purl.obolibrary.org/obo/GEO_000000371 geographical feature http://purl.obolibrary.org/obo/GEO_000000370 geographical entity Geographical entity that has at least one bona fide boundary. http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype http://purl.obolibrary.org/obo/BFO_0000019 quality The observable manifestation of the genotype of a microbial cell or group of cells in an environment. http://purl.obolibrary.org/obo/OMP_0000087 facultative anaerobe http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth but will utilize O2 in metabolic reactions when it is present. http://purl.obolibrary.org/obo/OMP_0000105 aerotolerant anaerobe http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype A microbial phenotype that describes a microorganism that does not require oxygen gas (O2) for growth and doesn't utilize O2 even when it is present. http://purl.obolibrary.org/obo/OMP_0000171 microaerophile http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype An oxygen growth range phenotype where growth and reproduction requires oxygen but at levels below that found in air (approx. 21%). A microbial phenotype that describes a microorganism that requires O2 for growth, but doesn't grow in the presence of atmospheric levels of O2. Optimal growth of a microaerophile occurs in environments with xx% - xx% O2. http://purl.obolibrary.org/obo/OMP_0000184 obligate anaerobe http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype A microbial phenotype that describes a microorganism that does not grow in the presence of oxygen gas (O2). http://purl.obolibrary.org/obo/OMP_0000185 obligate aerobe http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype A microbial phenotype that describes a microorganism that requires the presence of oxygen gas (O2) for growth. http://purl.obolibrary.org/obo/OMP_0000188 gram positive http://purl.obolibrary.org/obo/OMP_0000191 gram stain phenotype A gram stain phenotype where a cell or cells retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/OMP_0000189 gram negative http://purl.obolibrary.org/obo/OMP_0000191 gram stain phenotype A gram stain phenotype where a cell or cells do not retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/OMP_0000191 gram stain phenotype http://purl.obolibrary.org/obo/OMP_0000214 cell staining phenotype A cell staining phenotype where microorganisms are grouped based on their ability to retain crystal violet stain when decolorized with an organic solvent such as ethanol. http://purl.obolibrary.org/obo/OMP_0000199 acid-fast staining phenotype http://purl.obolibrary.org/obo/OMP_0000214 cell staining phenotype A cell-staining phenotype where a cell or cells are classified based on whether they are decolorized by an acid-alcohol mixture after staining, typically with carbolfuchsin. http://purl.obolibrary.org/obo/OMP_0000214 cell staining phenotype http://purl.obolibrary.org/obo/OMP_0000000 microbial phenotype A microbial phenotype where a cell or cells are treated with a dye or dyes for purposes of identification and classification. http://purl.obolibrary.org/obo/NCIT_C20464 cytokine http://purl.obolibrary.org/obo/PR_000000001 protein A class of soluble glycoproteins which act nonenzymatically through specific receptors to regulate immune responses. Cytokines are derived from both immune and non-immune cells and are intercellular mediators that differ from hormones in that they are produced by a number of tissue or cell types rather than by specialized glands. http://purl.obolibrary.org/obo/NCIT_C16459 complement system http://purl.obolibrary.org/obo/RO_0002577 system The complement system is a complex system of serum proteins that interact in a cascade. Many of the early components are serine proteases that activate each other sequentially. This complement system consists of three separate activation triggers: (1) Ab binding to a cell surface, (2) formation of immune complexes, and (3) a carbohydrate component of a microbe's cell membrane. Along with this triggers, there are also two sets of mechanisms. Both of these mechanisms, classical pathway and alternative or properdin pathway, make MAC (Membrane Attack Complex), which can lyse and destroy the cell. http://purl.obolibrary.org/obo/GO_0140367 antibacterial innate immune response http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium An defense response against a bacteria mediated through an innate immune response. An innate immune response is mediated by germline encoded components that directly recognize components of potential pathogens. http://purl.obolibrary.org/obo/CHEBI_3379 capsular polysaccharide http://purl.obolibrary.org/obo/CHEBI_18154 polysaccharide A polysaccharide capsule that is found on the cell surface of a broad range of bacterial species and often involved in mediating direct interactions between the bacteria and its environment. Due to these interactions, capsular polysaccharides have been implicated as important virulence factors for many bacterial pathogens. The molecules are highly hydrated and composed of repeating single monosaccharide units which are joined together by glycosidic linkages. They can be homo- or heteropolymers and can be substituted with organic molecules such as acetyl groups, or or inorganic molecules such as phosphate. http://purl.obolibrary.org/obo/CHEBI_75787 prokaryotic metabolite http://purl.obolibrary.org/obo/CHEBI_25212 metabolite Any metabolite produced during a metabolic reaction in prokaryotes, the taxon that include members of domains such as the bacteria and archaea. http://purl.obolibrary.org/obo/OMRSE_00000061 architectural structure http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity that is a human made structure with firm connection between its foundation and the ground. http://purl.obolibrary.org/obo/OMRSE_00000062 facility http://purl.obolibrary.org/obo/OMRSE_00000061 architectural structure Architectural structure that bears some function. http://purl.obolibrary.org/obo/OMRSE_00000063 hospital facility http://purl.obolibrary.org/obo/OMRSE_00000102 healthcare facility Facility that is run by a hospital organization and is the bearer of a hospital function. http://purl.obolibrary.org/obo/OMRSE_00000102 healthcare facility http://purl.obolibrary.org/obo/OMRSE_00000062 facility Facility that is administered by a health care organization for the purpose of providing health care to a patient or patient population. http://purl.obolibrary.org/obo/IDO_0001395 immunological memory http://purl.obolibrary.org/obo/BFO_0000027 object aggregate A population of memory B cells and memory T cells which bears an immunological memory disposition. http://purl.obolibrary.org/obo/IDO_0001372 epitope site http://purl.obolibrary.org/obo/BFO_0000029 site Site part of an antigen that is recognized by immune system cells and to which antibodies attach. http://purl.obolibrary.org/obo/OGMS_0000096 health care process http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient http://purl.obolibrary.org/obo/OGMS_0000098 hospitalization http://purl.obolibrary.org/obo/OGMS_0000097 health care encounter TODO http://purl.obolibrary.org/obo/IDO_0001088 acellular structure http://purl.obolibrary.org/obo/BFO_0000030 object Object consisting of an arrangement of interrelated acellular parts forming an acellular biological unit that is able to initiate replication of the structure in a host. http://purl.obolibrary.org/obo/IDO_0001030 parasitostatic disposition http://purl.obolibrary.org/obo/IDO_0001091 static agent disposition Disposition inhering in a material entity, that is realized in a process of inhibiting the reproduction of parasites. http://purl.obolibrary.org/obo/IDO_0001346 incubation end process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the end of an incubation period. http://purl.obolibrary.org/obo/IDO_0001110 infectious structure generative stage http://purl.obolibrary.org/obo/IDO_0001111 pathogen generative stage Pathogen generative stage that is a temporal subdivision of an infectious structure developmental process. http://purl.obolibrary.org/obo/IDO_0001163 cytotoxin disposition http://purl.obolibrary.org/obo/IDO_0000426 toxin disposition Toxin disposition realized in processes resulting in damage to host cells. http://purl.obolibrary.org/obo/TRANS_0000015 biologic pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000005 vector-borne pathogen transmission process Vector-borne pathogen transmission process during which the pathogen is transported, from a reservoir, source or host to another host, within the vector and undergoes part of it's lifecycle, or replication cycle, in the vector. http://purl.obolibrary.org/obo/IDO_0001354 latency start process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the start of a latency interval. http://purl.obolibrary.org/obo/IDO_0001111 pathogen generative stage http://purl.obolibrary.org/obo/IDO_0001112 generative stage Generative stage that is a temporal subdivision of a pathogen developmental process. http://purl.obolibrary.org/obo/IDO_0001172 infectious structure aggregate http://purl.obolibrary.org/obo/IDO_0001065 acellular structure aggregate Acellular structure aggregate whose members are infectious structures. http://purl.obolibrary.org/obo/GO_0000003 reproduction http://purl.obolibrary.org/obo/GO_0008150 biological process The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms. [database_cross_reference: GOC:go_curators][database_cross_reference: GOC:isa_complete][database_cross_reference: GOC:jl][database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/GO_0000269 toxin export channel activity http://purl.obolibrary.org/obo/GO_0019534 toxin transmembrane transporter activity Enables the energy independent passage of toxins, sized less than 1000 Da, across a membrane towards the outside of the cell. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. http://purl.obolibrary.org/obo/GO_0000910 cytokinesis http://purl.obolibrary.org/obo/GO_0022402 cell cycle process The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells. [database_cross_reference: GOC:mtg_cell_cycle] http://purl.obolibrary.org/obo/GO_0001061 bacterial-type RNA polymerase activity http://purl.obolibrary.org/obo/GO_0003899 DNA-directed 5'-3' RNA polymerase activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a bacterial-type specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001109 promoter clearance during DNA-templated transcription http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors. [database_cross_reference: PMID:15020047][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001112 DNA-templated transcription open complex formation http://purl.obolibrary.org/obo/GO_0043933 protein-containing complex subunit organization Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble. [database_cross_reference: PMID:15020047][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001121 bacterial transcription http://purl.obolibrary.org/obo/GO_0006351 transcription, DNA-templated The synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter. [database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001122 promoter clearance from bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0001109 promoter clearance during DNA-templated transcription Any process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001123 transcription initiation from bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0006352 DNA-templated transcription, initiation Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001124 transcription elongation from bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0006354 DNA-templated transcription, elongation The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001125 transcription termination from bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0006353 DNA-templated transcription, termination The process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001126 bacterial-type RNA polymerase preinitiation complex assembly http://purl.obolibrary.org/obo/GO_0070897 transcription preinitiation complex assembly The aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001127 transcription open complex formation at bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0001112 DNA-templated transcription open complex formation Any process involved in the melting of the DNA hybrid of the core promoter region within a bacterial-type RNA polymerase promoter to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble. [database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161] http://purl.obolibrary.org/obo/GO_0001173 DNA-templated transcriptional start site selection http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript. [database_cross_reference: PMID:16826228][database_cross_reference: PMID:18846104][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001176 transcriptional start site selection at bacterial-type RNA polymerase promoter http://purl.obolibrary.org/obo/GO_0001173 DNA-templated transcriptional start site selection Any process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript. [database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0001539 cilium or flagellum-dependent cell motility http://purl.obolibrary.org/obo/GO_0048870 cell motility Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella. http://purl.obolibrary.org/obo/GO_0001779 natural killer cell differentiation http://purl.obolibrary.org/obo/GO_0030101 natural killer cell activation The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/GO_0001787 natural killer cell proliferation http://purl.obolibrary.org/obo/GO_0030101 natural killer cell activation The expansion of a natural killer cell population by cell division. [database_cross_reference: GOC:add][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0001816 cytokine production http://purl.obolibrary.org/obo/GO_0010467 gene expression The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0001913 T cell mediated cytotoxicity http://purl.obolibrary.org/obo/GO_0002456 T cell mediated immunity The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors. http://purl.obolibrary.org/obo/GO_0002228 natural killer cell mediated immunity http://purl.obolibrary.org/obo/GO_0045087 innate immune response The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines. http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response http://purl.obolibrary.org/obo/GO_0006955 immune response Immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory). http://purl.obolibrary.org/obo/GO_0002319 memory B cell differentiation http://purl.obolibrary.org/obo/GO_0002313 mature B cell differentiation involved in immune response The process in which a B cell acquires the specialized features of a memory B cell. Memory B cells are cells that can respond rapidly to antigen re-exposure by production of high-affinity antibody. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/GO_0002335 mature B cell differentiation http://purl.obolibrary.org/obo/GO_0030183 B cell differentiation The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/GO_0002368 B cell cytokine production http://purl.obolibrary.org/obo/GO_0002367 cytokine production involved in immune response Any process that contributes to cytokine production by a B cell. http://purl.obolibrary.org/obo/GO_0002369 T cell cytokine production http://purl.obolibrary.org/obo/GO_0002367 cytokine production involved in immune response Any process that contributes to cytokine production by a T cell. http://purl.obolibrary.org/obo/GO_0002376 immune system process http://purl.obolibrary.org/obo/GO_0008150 biological process Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats. http://purl.obolibrary.org/obo/GO_0002443 leukocyte mediated immunity http://purl.obolibrary.org/obo/GO_0006955 immune response Process involved in the carrying out of an immune response by a leukocyte. http://purl.obolibrary.org/obo/GO_0002450 B cell antigen processing and presentation http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation The process in which a B cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0002456 T cell mediated immunity http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process involved in the carrying out of an immune response by a T cell. http://purl.obolibrary.org/obo/GO_0002457 T cell antigen processing and presentation http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation The process in which a T cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus. http://purl.obolibrary.org/obo/GO_0002468 dendritic cell antigen processing and presentation http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation The process in which a dendritic cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0002471 monocyte antigen processing and presentation http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation The process in which a monocyte expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0002472 macrophage antigen processing and presentation http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation The process in which a macrophage expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0003674 molecular_function http://purl.obolibrary.org/obo/BFO_0000015 process A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. http://purl.obolibrary.org/obo/GO_0003823 antigen binding http://purl.obolibrary.org/obo/GO_0003674 molecular_function Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. http://purl.obolibrary.org/obo/GO_0003824 catalytic activity http://purl.obolibrary.org/obo/GO_0003674 molecular_function Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. [database_cross_reference: GOC:vw][database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/GO_0003899 DNA-directed 5'-3' RNA polymerase activity http://purl.obolibrary.org/obo/GO_0034062 5'-3' RNA polymerase activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. [database_cross_reference: GOC:pf][database_cross_reference: EC:2.7.7.6] http://purl.obolibrary.org/obo/GO_0005737 cytoplasm http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. http://purl.obolibrary.org/obo/GO_0005840 ribosome http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. [database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/GO_0005886 plasma membrane http://purl.obolibrary.org/obo/GO_0016020 membrane The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. http://purl.obolibrary.org/obo/GO_0005887 integral component of plasma membrane http://purl.obolibrary.org/obo/GO_0031224 intrinsic component of membrane The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane. http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process http://purl.obolibrary.org/obo/GO_0090304 nucleic acid metabolic process Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides. http://purl.obolibrary.org/obo/GO_0006260 DNA replication http://purl.obolibrary.org/obo/GO_0034645 cellular macromolecule biosynthetic process The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA. http://purl.obolibrary.org/obo/GO_0006266 DNA ligation http://purl.obolibrary.org/obo/GO_0006259 DNA metabolic process The re-formation of a broken phosphodiester bond in the DNA backbone, carried out by DNA ligase. http://purl.obolibrary.org/obo/GO_0006351 transcription, DNA-templated http://purl.obolibrary.org/obo/GO_0097659 nucleic acid-templated transcription The cellular synthesis of RNA on a template of DNA. [database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0006352 DNA-templated transcription, initiation http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription. [database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jid] http://purl.obolibrary.org/obo/GO_0006353 DNA-templated transcription, termination http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA. [database_cross_reference: PMID:15020047][database_cross_reference: ISBN:0716720094][database_cross_reference: PMID:18280161][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0006354 DNA-templated transcription, elongation http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase. [database_cross_reference: PMID:15020047][database_cross_reference: GOC:txnOH][database_cross_reference: PMID:18280161][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0006909 phagocytosis http://purl.obolibrary.org/obo/GO_0016192 vesicle-mediated transport A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles. http://purl.obolibrary.org/obo/GO_0006952 defense response http://purl.obolibrary.org/obo/GO_0008150 biological process Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack. http://purl.obolibrary.org/obo/GO_0006954 inflammatory response http://purl.obolibrary.org/obo/GO_0006952 defense response The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. http://purl.obolibrary.org/obo/GO_0006955 immune response http://purl.obolibrary.org/obo/GO_0002376 immune system process Immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. http://purl.obolibrary.org/obo/GO_0006959 humoral immune response http://purl.obolibrary.org/obo/GO_0006955 immune response Immune response mediated through a body fluid. http://purl.obolibrary.org/obo/GO_0007049 cell cycle http://purl.obolibrary.org/obo/GO_0009987 cellular process The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division. http://purl.obolibrary.org/obo/GO_0007154 cell communication http://purl.obolibrary.org/obo/GO_0009987 cellular process Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment. http://purl.obolibrary.org/obo/GO_0007267 cell-cell signaling http://purl.obolibrary.org/obo/GO_0007154 cell communication Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions. http://purl.obolibrary.org/obo/GO_0008150 biological process http://purl.obolibrary.org/obo/BFO_0000015 process Process specifically pertinent to the functioning of functionally integrated units. http://purl.obolibrary.org/obo/GO_0009306 protein secretion http://purl.obolibrary.org/obo/GO_0015031 protein transport The controlled release of proteins from a cell. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/GO_0009987 cellular process http://purl.obolibrary.org/obo/GO_0008150 biological process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. http://purl.obolibrary.org/obo/GO_0010467 gene expression http://purl.obolibrary.org/obo/GO_0043170 macromolecule metabolic process The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. [database_cross_reference: GOC:dph][database_cross_reference: GOC:tb] http://purl.obolibrary.org/obo/GO_0015288 porin activity http://purl.obolibrary.org/obo/GO_0022829 wide pore channel activity Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. http://purl.obolibrary.org/obo/GO_0015833 peptide transport http://purl.obolibrary.org/obo/GO_0006810 transport The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response http://purl.obolibrary.org/obo/GO_0019724 B cell mediated immunity An immune response mediated by immunoglobulins, whether cell-bound or in solution. http://purl.obolibrary.org/obo/GO_0016070 RNA metabolic process http://purl.obolibrary.org/obo/GO_0090304 nucleic acid metabolic process The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. [database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/GO_0019534 toxin transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0022857 transmembrane transporter activity Enables the transfer of a toxin from one side of a membrane to the other. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/GO_0019724 B cell mediated immunity http://purl.obolibrary.org/obo/GO_0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells. http://purl.obolibrary.org/obo/GO_0019730 antimicrobial humoral response http://purl.obolibrary.org/obo/GO_0006959 humoral immune response An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus. http://purl.obolibrary.org/obo/GO_0019731 antibacterial humoral response http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster. http://purl.obolibrary.org/obo/GO_0019882 antigen processing and presentation http://purl.obolibrary.org/obo/GO_0002376 immune system process The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex. http://purl.obolibrary.org/obo/GO_0019954 asexual reproduction http://purl.obolibrary.org/obo/GO_0000003 reproduction The biological process in which new individuals are produced by either a single cell or a group of cells, in the absence of any sexual process. [database_cross_reference: ISBN:0387520546] http://purl.obolibrary.org/obo/GO_0022607 cellular component assembly http://purl.obolibrary.org/obo/GO_0016043 cellular component organization The aggregation, arrangement and bonding together of a cellular component. [database_cross_reference: GOC:isa_complete] http://purl.obolibrary.org/obo/GO_0030101 natural killer cell activation http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0030183 B cell differentiation http://purl.obolibrary.org/obo/GO_0042113 B cell activation The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. [database_cross_reference: GO_REF:0000022][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0030217 T cell differentiation http://purl.obolibrary.org/obo/GO_0042110 T cell activation The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex. [database_cross_reference: GOC:mah][database_cross_reference: GO_REF:0000022][database_cross_reference: GOC:jid] http://purl.obolibrary.org/obo/GO_0032502 developmental process http://purl.obolibrary.org/obo/GO_0008150 biological process Biological process whose specific outcome is the progression of a functional, integrated, unit. http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process http://purl.obolibrary.org/obo/GO_0016070 RNA metabolic process The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication. [database_cross_reference: GOC:mah][database_cross_reference: GOC:txnOH] http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex http://purl.obolibrary.org/obo/BFO_0000040 material entity Stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. http://purl.obolibrary.org/obo/GO_0034062 5'-3' RNA polymerase activity http://purl.obolibrary.org/obo/GO_0097747 RNA polymerase activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 3'-end. [database_cross_reference: EC:2.7.7.6][database_cross_reference: GOC:pf][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0034622 cellular protein-containing complex assembly http://purl.obolibrary.org/obo/GO_0065003 protein-containing complex assembly The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0042098 T cell proliferation http://purl.obolibrary.org/obo/GO_0042110 T cell activation The expansion of a T cell population by cell division. Follows T cell activation. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0042100 B cell proliferation http://purl.obolibrary.org/obo/GO_0042113 B cell activation The expansion of a B cell population by cell division. Follows B cell activation. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0042110 T cell activation http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. http://purl.obolibrary.org/obo/GO_0042113 B cell activation http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0042546 cell wall biogenesis http://purl.obolibrary.org/obo/GO_0044085 cellular component biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall. Includes biosynthesis of constituent macromolecules, such as proteins and polysaccharides, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. A cell wall is the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mah][database_cross_reference: GOC:mtg_sensu][database_cross_reference: ISBN:0198506732] http://purl.obolibrary.org/obo/GO_0042995 cell projection http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A prolongation or process extending from a cell, e.g. a flagellum or axon. http://purl.obolibrary.org/obo/GO_0043226 organelle http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043228 non-membrane-bounded organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/GO_0043933 protein-containing complex subunit organization http://purl.obolibrary.org/obo/GO_0016043 cellular component organization Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0045087 innate immune response http://purl.obolibrary.org/obo/GO_0006955 immune response Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. http://purl.obolibrary.org/obo/GO_0046649 lymphocyte activation http://purl.obolibrary.org/obo/GO_0009987 cellular process A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor. [database_cross_reference: GOC:mgi_curators][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0048519 negative regulation of biological process http://purl.obolibrary.org/obo/GO_0065007 biological regulation Process that stops, prevents, or reduces the frequency, rate or extent of a biological process. http://purl.obolibrary.org/obo/GO_0048870 cell motility http://purl.obolibrary.org/obo/GO_0009987 cellular process Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another. http://purl.obolibrary.org/obo/GO_0050777 negative regulation of immune response http://purl.obolibrary.org/obo/GO_0048519 negative regulation of biological process Process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus. http://purl.obolibrary.org/obo/GO_0050829 defense response to Gram-negative bacterium http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/GO_0050830 defense response to Gram-positive bacterium http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/GO_0051093 negative regulation of developmental process http://purl.obolibrary.org/obo/GO_0048519 negative regulation of biological process Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult). http://purl.obolibrary.org/obo/GO_0051301 cell division http://purl.obolibrary.org/obo/GO_0009987 cellular process The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells. http://purl.obolibrary.org/obo/GO_0065004 protein-DNA complex assembly http://purl.obolibrary.org/obo/GO_0034622 cellular protein-containing complex assembly The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex. [database_cross_reference: GOC:jl] http://purl.obolibrary.org/obo/GO_0070897 transcription preinitiation complex assembly http://purl.obolibrary.org/obo/GO_0065004 protein-DNA complex assembly The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), required for transcription. [database_cross_reference: GOC:txnOH][database_cross_reference: GOC:jp] http://purl.obolibrary.org/obo/GO_0097659 nucleic acid-templated transcription http://purl.obolibrary.org/obo/GO_0032774 RNA biosynthetic process The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA). [database_cross_reference: GOC:pr][database_cross_reference: GOC:txnOH][database_cross_reference: GOC:vw] http://purl.obolibrary.org/obo/GO_0098630 aggregation of unicellular organisms http://purl.obolibrary.org/obo/GO_0098743 cell aggregation The clustering together of unicellular organisms in suspension form aggregates. http://purl.obolibrary.org/obo/GO_0098743 cell aggregation http://purl.obolibrary.org/obo/GO_0009987 cellular process The clustering together and adhesion of initially separate cells to form an aggregate. Examples include the clustering of unicellular organisms or blood cells in suspension and the condensation of mesenchymal cells during cartilage formation. http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex Protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0019815 B cell receptor complex http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex Immunoglobulin complex present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. http://purl.obolibrary.org/obo/GO_0020033 antigenic variation http://purl.obolibrary.org/obo/GO_0042783 evasion of host immune response Any process involved in the biological strategy of changing antigenic determinants on the surface that are exposed to another organism's immune system. http://purl.obolibrary.org/obo/GO_0030075 bacterial thylakoid http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle A thylakoid that is derived from and attached to, but not necessarily continuous with, the plasma membrane, and is not enclosed in a plastid. It bears the photosynthetic pigments in photosynthetic cyanobacteria. http://purl.obolibrary.org/obo/GO_0030112 glycocalyx http://purl.obolibrary.org/obo/GO_0030312 external encapsulating structure A carbohydrate rich layer at the outermost periphery of a cell. [database_cross_reference: GOC:krc][database_cross_reference: ISBN:0815316208][database_cross_reference: GOC:mlg][database_cross_reference: PMID:28876829] http://purl.obolibrary.org/obo/GO_0030114 slime layer http://purl.obolibrary.org/obo/GO_0030112 glycocalyx A slime layer is an easily removed, diffuse, unorganized layer of extracellular material that surrounds a cell. Specifically this consists mostly of exopolysaccharides, glycoproteins, and glycolipids. [database_cross_reference: GOC:mlg][database_cross_reference: Wikipedia:Slime_layer] http://purl.obolibrary.org/obo/GO_0030115 S-layer http://purl.obolibrary.org/obo/GO_0030312 external encapsulating structure A crystalline protein layer surrounding some bacteria. [database_cross_reference: GOC:mlg][database_cross_reference: ISBN:0815108893] http://purl.obolibrary.org/obo/GO_0030152 bacteriocin biosynthetic process http://purl.obolibrary.org/obo/GO_0009403 toxin biosynthetic process The chemical reactions and pathways resulting in the formation of a bacteriocin, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. http://purl.obolibrary.org/obo/GO_0030253 protein secretion by the type I secretion system http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which proteins are secreted into the extracellular milieu via the type I secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0030254 protein secretion by the type III secretion system http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which proteins are transferred into the extracellular milieu or directly into host cells by the bacterial type III secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0030255 protein secretion by the type IV secretion system http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type IV protein secretion system. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0030256 type I protein secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space. [database_cross_reference: PMID:9618447] http://purl.obolibrary.org/obo/GO_0030257 type III protein secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A complex of approximately 20 proteins, most of which are located in the cytoplasmic membrane that carries out protein secretion in the bacterial type III secretion system; type III secretion also requires a cytoplasmic, probably membrane-associated ATPase. [database_cross_reference: PMID:9618447] http://purl.obolibrary.org/obo/GO_0031469 polyhedral organelle http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle An organelle found in bacteria consisting of a proteinaceous coat containing metabolic enzymes whose purpose is the sequestration or concentration of metabolites and which has the appearance of a polygonal granule by electron microscopy. [database_cross_reference: GOC:js][database_cross_reference: PMID:10498708][database_cross_reference: PMID:11844753][database_cross_reference: PMID:12923081] http://purl.obolibrary.org/obo/GO_0031470 carboxysome http://purl.obolibrary.org/obo/GO_0031469 polyhedral organelle An organelle consisting of a proteinaceous coat and enzymes for the fixation of CO(2). It augments the concentration of CO(2) in the vicinity of RuBisCO to increase the efficiency of CO(2) fixation under atmospheric conditions. [database_cross_reference: GOC:js][database_cross_reference: PMID:8157606][database_cross_reference: PMID:8491708][database_cross_reference: PMID:28934381] http://purl.obolibrary.org/obo/GO_0031471 ethanolamine degradation polyhedral organelle http://purl.obolibrary.org/obo/GO_0031469 polyhedral organelle An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of ethanolamine whose purpose is the protection of the rest of the cell from the toxic acetaldehyde product of the enzyme ethanolamine ammonia lyase. [database_cross_reference: GOC:js][database_cross_reference: PMID:11844753] http://purl.obolibrary.org/obo/GO_0031472 propanediol degradation polyhedral organelle http://purl.obolibrary.org/obo/GO_0031469 polyhedral organelle An organelle found in bacteria consisting of a proteinaceous coat containing enzymes for the degradation of 1,2-propanediol whose purpose is the protection of the rest of the cell from the toxic propionaldehyde product of the enzyme diol dehydratase. [database_cross_reference: GOC:js][database_cross_reference: PMID:10498708][database_cross_reference: PMID:11844753][database_cross_reference: PMID:12923081] http://purl.obolibrary.org/obo/GO_0031522 cell envelope Sec protein transport complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A transmembrane protein complex involved in the translocation of proteins across the cytoplasmic membrane. In Gram-negative bacteria, Sec-translocated proteins are subsequently secreted via the type II, IV, or V secretion systems. Sec complex components include SecA, D, E, F, G, Y and YajC. [database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:15223057] http://purl.obolibrary.org/obo/GO_0031975 envelope http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers. http://purl.obolibrary.org/obo/GO_0032602 chemokine production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria. http://purl.obolibrary.org/obo/GO_0032606 type I interferon production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families. http://purl.obolibrary.org/obo/GO_0032607 interferon-alpha production http://purl.obolibrary.org/obo/GO_0032606 type I interferon production The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032608 interferon-beta production http://purl.obolibrary.org/obo/GO_0032606 type I interferon production The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032609 interferon-gamma production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon. http://purl.obolibrary.org/obo/GO_0032612 interleukin-1 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032613 interleukin-10 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032614 interleukin-11 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032615 interleukin-12 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032616 interleukin-13 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032617 interleukin-14 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032618 interleukin-15 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032619 interleukin-16 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032620 interleukin-17 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032623 interleukin-2 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032632 interleukin-3 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032633 interleukin-4 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032634 interleukin-5 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032635 interleukin-6 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032637 interleukin-8 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0032638 interleukin-9 production http://purl.obolibrary.org/obo/GO_0001816 cytokine production The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0033103 protein secretion by the type VI secretion system http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which proteins are transferred into the extracellular milieu or directly into host cells by the type VI secretion system. Proteins secreted by this system do not require an N-terminal signal sequence. [database_cross_reference: GOC:mlg][database_cross_reference: PMID:16432199][database_cross_reference: PMID:16763151] http://purl.obolibrary.org/obo/GO_0033104 type VI protein secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A complex of proteins that permits the transfer of proteins into the extracellular milieu or directly into host cells via the type VI secretion system. Proteins secreted by this complex do not require an N-terminal signal sequence. [database_cross_reference: GOC:mlg][database_cross_reference: PMID:16432199][database_cross_reference: PMID:16763151] http://purl.obolibrary.org/obo/GO_0033281 TAT protein transport complex http://purl.obolibrary.org/obo/GO_0098797 plasma membrane protein complex A complex of three proteins integral to the cytoplasmic membrane of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) involved in membrane transport of folded proteins. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0042603 capsule http://purl.obolibrary.org/obo/GO_0030112 glycocalyx A protective structure surrounding some fungi and bacteria, attached externally to the cell wall and composed primarily of polysaccharides. Capsules are highly organized structures that adhere strongly to cells and cannot be easily removed. Capsules play important roles in pathogenicity, preventing phagocytosis by other cells, adherance, and resistance to dessication. [database_cross_reference: GOC:mlg] http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen. http://purl.obolibrary.org/obo/GO_0043227 membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043226 organelle Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. http://purl.obolibrary.org/obo/GO_0044406 adhesion of symbiont to host http://purl.obolibrary.org/obo/GO_0022610 biological adhesion Attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. http://purl.obolibrary.org/obo/GO_0046224 bacteriocin metabolic process http://purl.obolibrary.org/obo/GO_0009404 toxin metabolic process The chemical reactions and pathways involving bacteriocins, any of a heterogeneous group of polypeptide antibiotics that are secreted by certain bacterial strains and are able to kill cells of other susceptible (frequently related) strains after adsorption at specific receptors on the cell surface. They include the colicins, and their mechanisms of action vary. [database_cross_reference: GOC:ai] http://purl.obolibrary.org/obo/GO_0097747 RNA polymerase activity http://purl.obolibrary.org/obo/GO_0003824 catalytic activity Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template. [database_cross_reference: GOC:pf] http://purl.obolibrary.org/obo/GO_1901998 toxin transport http://purl.obolibrary.org/obo/GO_0006810 transport The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. http://purl.obolibrary.org/obo/GO_1990904 ribonucleoprotein complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A macromolecular complex that contains both RNA and protein molecules. [database_cross_reference: GOC:krc][database_cross_reference: GOC:vesicles] http://purl.obolibrary.org/obo/GO_0035635 entry of bacterium into host cell http://purl.obolibrary.org/obo/GO_0044409 entry into host The process in which a bacterium enters a host cell. http://purl.obolibrary.org/obo/GO_0036407 mycolate outer membrane http://purl.obolibrary.org/obo/GO_0009279 cell outer membrane A mycolic acid-rich cell outer membrane containing a lipid bilayer and long-chain mycolic acids (hydroxylated branched-chain fatty acids) that are covalently linked to the cell wall peptidoglycan via an arabinogalactan network. Found in mycobacteria and related genera (e.g. corynebacteria). http://purl.obolibrary.org/obo/GO_0038197 type I interferon receptor complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A heterodimeric protein complex that binds a type I interferon and transmits the signal across the membrane into the cell. Consists of an alpha subunit (IFNAR1) and a beta subunit (IFNAR2). http://purl.obolibrary.org/obo/GO_0042000 translocation of peptides or proteins into host http://purl.obolibrary.org/obo/GO_0044417 translocation of molecules into host The directed movement of peptides or proteins produced by an organism to a location inside its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:cc] http://purl.obolibrary.org/obo/GO_0042101 T cell receptor complex http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex Protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains. http://purl.obolibrary.org/obo/GO_0042612 MHC class I protein complex http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules. http://purl.obolibrary.org/obo/GO_0042613 MHC class II protein complex http://purl.obolibrary.org/obo/GO_0042611 MHC protein complex A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen. http://purl.obolibrary.org/obo/GO_0042710 biofilm formation http://purl.obolibrary.org/obo/GO_0098630 aggregation of unicellular organisms A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription. http://purl.obolibrary.org/obo/GO_0042783 evasion of host immune response http://purl.obolibrary.org/obo/GO_0008150 biological process Process by which an organism or acellular structure avoids the effects of the host organism's immune response. http://purl.obolibrary.org/obo/GO_0043093 FtsZ-dependent cytokinesis http://purl.obolibrary.org/obo/GO_0000910 cytokinesis A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells. [database_cross_reference: GOC:mah][database_cross_reference: ISBN:0815108893][database_cross_reference: PMID:12626683] http://purl.obolibrary.org/obo/GO_0043107 type IV pilus-dependent motility http://purl.obolibrary.org/obo/GO_0048870 cell motility Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility. http://purl.obolibrary.org/obo/GO_0043152 induction of bacterial agglutination http://purl.obolibrary.org/obo/GO_0019731 antibacterial humoral response Any process in which infecting bacteria are clumped together by a host organism. http://purl.obolibrary.org/obo/GO_0043164 Gram-negative-bacterium-type cell wall biogenesis http://purl.obolibrary.org/obo/GO_0009273 peptidoglycan-based cell wall biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Gram-negative bacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mtg_sensu][database_cross_reference: ISBN:0815108893] http://purl.obolibrary.org/obo/GO_0043379 memory T cell differentiation http://purl.obolibrary.org/obo/GO_0002292 T cell differentiation involved in immune response The process in which a newly activated T cell acquires specialized features of a memory T cell. [database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0043514 interleukin-12 complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A protein complex that is composed of an interleukin-12 alpha (p35, product of the IL12A gene) and an interleukin-12 beta subunit (p40, product of the IL12B gene) and is secreted into the extracellular space. http://purl.obolibrary.org/obo/GO_0043590 bacterial nucleoid http://purl.obolibrary.org/obo/GO_0043232 intracellular non-membrane-bounded organelle The region of a bacterial cell to which the DNA is confined. http://purl.obolibrary.org/obo/GO_0043684 type IV secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A complex of proteins related to those involved in bacterial DNA conjugative transfer, that permits the transfer of DNA or proteins into the extracellular milieu or directly into host cells. In general the type IV complex forms a multisubunit cell-envelope-spanning structure composed of a secretion channel and often a pilus or other surface filament or protein(s). [database_cross_reference: GOC:ml] http://purl.obolibrary.org/obo/GO_0043952 protein transport by the Sec complex http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0043953 protein transport by the Tat complex http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which folded proteins are transported across cytoplasmic membranes of bacteria and membranes of organelles derived from bacteria (chloroplasts and mitochondria) by the TAT complex. [database_cross_reference: GOC:pamgo_curators] http://purl.obolibrary.org/obo/GO_0044053 translocation of peptides or proteins into host cell cytoplasm http://purl.obolibrary.org/obo/GO_0042000 translocation of peptides or proteins into host The directed movement of peptides or proteins produced by a symbiont organism to a location within the host cell cytoplasm. [database_cross_reference: MITRE:tk] http://purl.obolibrary.org/obo/GO_0044315 protein secretion by the type VII secretion system http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The process in which proteins are transferred into the extracellular milieu or directly into host cells, via the type VII protein secretion system. [database_cross_reference: PMID:17922044][database_cross_reference: PMID:19876390] http://purl.obolibrary.org/obo/GO_0044417 translocation of molecules into host http://purl.obolibrary.org/obo/GO_0008150 biological process The directed movement of a molecule(s) produced by an organism to a location inside its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:cc] http://purl.obolibrary.org/obo/GO_0044787 bacterial-type DNA replication http://purl.obolibrary.org/obo/GO_0044786 cell cycle DNA replication The DNA-dependent DNA replication, exemplified by prokaryotes, that occurs as part of the cell cycle. Prokaryotic DNA replication is bi-directional and originates at a single origin of replication on the circular genome. http://purl.obolibrary.org/obo/GO_0048525 negative regulation of viral process http://purl.obolibrary.org/obo/GO_0048519 negative regulation of biological process Process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant. http://purl.obolibrary.org/obo/GO_0070726 cell wall assembly http://purl.obolibrary.org/obo/GO_0022607 cellular component assembly The aggregation, arrangement and bonding together of a cell wall. A cell wall is a rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells. [database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0090716 adaptive immune memory response http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response An immune response directed against a previously encountered antigen, being quicker and quantitatively better compared with the primary response. http://purl.obolibrary.org/obo/GO_0090717 adaptive immune memory response involving T cells and B cells http://purl.obolibrary.org/obo/GO_0090716 adaptive immune memory response An immune response mediated by reactivated memory T cells and B cells and directed against a previously encountered antigen, being quicker and quantitatively better compared with the primary response. http://purl.obolibrary.org/obo/GO_0090720 primary adaptive immune response http://purl.obolibrary.org/obo/GO_0002250 adaptive immune response An adaptive immune response against an antigen not previously encountered by immune system. http://purl.obolibrary.org/obo/GO_0097281 immune complex formation http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus. http://purl.obolibrary.org/obo/GO_0097282 immunoglobulin-mediated neutralization http://purl.obolibrary.org/obo/GO_0016064 immunoglobulin mediated immune response The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin. [database_cross_reference: GOC:add][database_cross_reference: GOC:rv] http://purl.obolibrary.org/obo/GO_0097311 bacterial biofilm matrix http://purl.obolibrary.org/obo/GO_0062039 biofilm matrix A structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria. http://purl.obolibrary.org/obo/GO_0097313 bacterial biofilm matrix surface http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The external part of the biofilm matrix, a structure lying external to bacterial cells. A biofilm is an aggregate of surface-associated bacteria, and the biofilm matrix is the envelope of polymeric substances that surrounds the bacteria. http://purl.obolibrary.org/obo/GO_0097347 TAM protein secretion complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A heterooligomeric protein complex that spans the bacterial periplasm and enables the secretion of adhesin proteins in Gram-negative bacteria. In Citrobacter rodentium, Salmonella enterica and Escherichia coli, the TAM complex consists of an Omp85-family protein, TamA, in the outer membrane and TamB in the inner membrane. [database_cross_reference: GOC:am][database_cross_reference: PMID:22466966] http://purl.obolibrary.org/obo/GO_0097691 bacterial extracellular vesicle http://purl.obolibrary.org/obo/GO_1903561 extracellular vesicle Small membrane vesicle (< 1 um) that buds off a prokaryotic cell plasma membrane, able to carry proteins, phospholipids, lipopolysaccharides, nucleic acids, viruses, and more. Important in intercellular communication and pathogenesis; can exist within host cells. http://purl.obolibrary.org/obo/GO_0098046 type V protein secretion system complex http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A complex of proteins that permits the translocation of proteins across the outer membrane via a transmembrane pore, formed by a beta-barrel, into the extracellular milieu or directly into host cells; the secreted proteins contain all the information required for translocation of an effector molecule through the cell envelope. The type V secretion systems includes the autotransporters (type Va), the two-partner secretion system (type Vb) and the Oca family (type Vc). [database_cross_reference: PMID:15590781][database_cross_reference: GOC:bf][database_cross_reference: GOC:bhm][database_cross_reference: PMID:15119822] http://purl.obolibrary.org/obo/GO_0098774 curli http://purl.obolibrary.org/obo/GO_0032991 protein-containing complex A proteinaceous extracellular fiber, produced by an enteric bacterium, that is involved in surface and cell-cell contacts that promote community behavior and host colonization. http://purl.obolibrary.org/obo/GO_0098777 protein secretion by the type VIII secretion system http://purl.obolibrary.org/obo/GO_0098776 protein transport across the cell outer membrane Protein secretion through the outer membrane via the mechanism used for the secretion of curli subunits. [database_cross_reference: PMID:24080089][database_cross_reference: PMID:19299134] http://purl.obolibrary.org/obo/GO_0098784 biofilm matrix organization http://purl.obolibrary.org/obo/GO_0030198 extracellular matrix organization A process that results in the assembly, arrangement of constituent parts, or disassembly of a biofilm matrix. http://purl.obolibrary.org/obo/GO_0098785 biofilm matrix assembly http://purl.obolibrary.org/obo/GO_0098784 biofilm matrix organization A process that results in the assembly of a biofilm matrix. http://purl.obolibrary.org/obo/GO_0098786 biofilm matrix disassembly http://purl.obolibrary.org/obo/GO_0098784 biofilm matrix organization A process that results in the disassembly of a biofilm matrix. http://purl.obolibrary.org/obo/GO_1902291 cell cycle DNA replication DNA ligation http://purl.obolibrary.org/obo/GO_0051104 DNA-dependent DNA replication DNA ligation Any DNA ligation that is involved in cell cycle DNA replication. http://purl.obolibrary.org/obo/GO_1902327 bacterial-type DNA replication DNA ligation http://purl.obolibrary.org/obo/GO_1902291 cell cycle DNA replication DNA ligation Any DNA ligation that is involved in bacterial-type DNA replication. http://purl.obolibrary.org/obo/PR_000000017 interferon gamma http://purl.obolibrary.org/obo/PR_000024990 type II interferon A type II interferon that is a translation product of the human IFNG gene or a 1:1 ortholog thereof. The core domain structure consists of an Interferon gamma domain (Pfam:PF00714) that is four-helical cytokine domain with an additional helix in one of the crossover connections. It is a cytokine produced by lymphocytes activated by specific antigens or mitogens that has important immunoregulatory functions. http://purl.obolibrary.org/obo/PR_000001091 interleukin-1 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein with a core domain composition consisting of a propeptide region and an Interleukin-1 / 18 domain. http://purl.obolibrary.org/obo/PR_000001092 interleukin-17 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a T cell-derived cytokine that may play an important role in the initiation or maintenance of the proinflammatory response. Except for IL-17B, all other IL-17 family members are homodimers containing five highly conserved cysteine residues forming characteristic cystein-knot structure, similar to that found in the TGF-beta-like cystine-knot (PR:000000008). This class consists of six cytokines. Among them, interleukin 17A (IL-17) and IL-17F are expressed by a novel subset of CD4+ helper T (Th) cells and play a critical role in inflammation and autoimmunity. On the other hand, IL-17E, also called IL-25, has been associated with allergic responses. http://purl.obolibrary.org/obo/PR_000001096 Toll-like receptor http://purl.obolibrary.org/obo/PR_000000001 protein A protein with a core domain composition consisting of a signal peptide, an extracellular domain with multiple Leucine rich repeat (Pfam:PF13855) domain (LRR), a cysteine-rich region, a single-pass transmembrane domain and a C-terminal cytoplasmic tail containing a TIR domain (Pfam:PF01582). http://purl.obolibrary.org/obo/PR_000001317 interleukin-7 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL7 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001335 class 2 cytokine, IL-10 type http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein with a core domain architecture consisting of an N-terminal Interleukin 10 (Pfam:PF00726) domain. http://purl.obolibrary.org/obo/PR_000001362 interferon lambda http://purl.obolibrary.org/obo/PR_000028205 type III interferon A type III interferon that is distantly related to type I interferons (IFNs) and the interleukin-10 family. It comprises the translation product of the IL28A, IL28B and IL29 genes. Generally induced by viral infection and exert their antiviral and immunomodulatory activities through a unique receptor complex composed of IFN-lambdaR1 and interleukin 10 receptor 2. http://purl.obolibrary.org/obo/PR_000001366 interleukin-11 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL11 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001368 interleukin-12 subunit alpha http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL12A gene or a 1:1 ortholog thereof. It associates with interleukin-12 subunit beta to form the interleukin-23. Interleukin-12 subunit alpha associates with interleukin-27 subunit beta to form the interleukin-35. http://purl.obolibrary.org/obo/PR_000001369 interleukin-12 subunit beta http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL12B gene or a 1:1 ortholog thereof. Interleukin-12 subunit beta associates with interleukin-12 subunit alpha or interleukin-23 subunit alpha to form the interleukin-23. http://purl.obolibrary.org/obo/PR_000001370 interleukin-13 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine protein that is a translation product of the human IL13 gene or a 1:1 ortholog thereof. Interleukin-13 is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related. http://purl.obolibrary.org/obo/PR_000001373 interleukin-15 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL15 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001374 interleukin-16 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL16 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001379 interleukin-2 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL2 gene or a 1:1 ortholog thereof. Interleukin-2 has a dual role in maintaining tolerance and contributing to immunity. http://purl.obolibrary.org/obo/PR_000001387 interleukin-3 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL3 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001391 interleukin-4 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL4 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001392 interleukin-5 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL5 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001393 interleukin-6 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001395 interleukin-8 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human CXCL8 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001396 interleukin-9 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that is a translation product of the human IL9 gene or a 1:1 ortholog thereof. http://purl.obolibrary.org/obo/PR_000001471 interleukin-10 http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A class 2 cytokine, IL-10 type that is a translation product of the human IL10 gene or a 1:1 ortholog thereof. Active interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. Structurally, IL-10 is a protein of about 160 amino acids that contains four conserved cysteines involved in disulfide bonds. http://purl.obolibrary.org/obo/PR_000024990 type II interferon http://purl.obolibrary.org/obo/NCIT_C20464 cytokine A protein that binds to a specific cell surface receptor complex known as the IFN-gamma receptor (IFNGR), a complex of two IFNGR1 and two IFNGR2 chains. http://purl.obolibrary.org/obo/PR_000028205 type III interferon http://purl.obolibrary.org/obo/PR_000001335 class 2 cytokine, IL-10 type A class 2 cytokine, IL-10 type that binds to a specific cell surface receptor complex known as the IFN type III receptor, a heterodimer consisting of IFNLR1 and IL-10R2. http://purl.obolibrary.org/obo/PR_000023923 protein translocase subunit SecA http://purl.obolibrary.org/obo/PR_000000001 protein A protein that is a translation product of the Escherichia coli K-12 secA gene or a 1:1 ortholog thereof. [database_cross_reference: PRO:DNx] http://purl.obolibrary.org/obo/ENVO_01000254 enviromental system http://purl.obolibrary.org/obo/RO_0002577 system A system which has the disposition to environ one or more material entities. http://purl.obolibrary.org/obo/RO_0002577 system http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity consisting of multiple components that are causally integrated. http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit http://purl.obolibrary.org/obo/UO_0000000 unit A unit which is a standard measure of physical quantity consisting of only a numerical number without any units. http://purl.obolibrary.org/obo/UO_0000189 count unit http://purl.obolibrary.org/obo/UO_0000186 dimensionless unit A dimensionless unit which denotes a simple count of things. http://purl.obolibrary.org/obo/UO_0000213 colony forming unit per milliliter http://purl.obolibrary.org/obo/UO_0000212 colony forming unit per volume A colony forming unit which a measure of viable bacterial numbers in one milliliter. http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity http://purl.obolibrary.org/obo/GO_0005575 cellular_component A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex. http://purl.obolibrary.org/obo/IDO_0001164 neurotoxin disposition http://purl.obolibrary.org/obo/IDO_0000426 toxin disposition Toxin disposition realized in damaging or interfering with the function of nerve tissue. http://purl.obolibrary.org/obo/IDO_0001133 symptomatic carrier role http://purl.obolibrary.org/obo/IDO_0000415 pathogen host role Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has manifested symptoms of the infectious disease caused by the pathogen. http://purl.obolibrary.org/obo/IDO_0001374 epitope role http://purl.obolibrary.org/obo/CHEBI_24432 biological role Biological role borne by a material entity that serves as the site on an antigen realized in immune system recognition and binding by antibodies. http://purl.obolibrary.org/obo/GO_0009061 anaerobic respiration http://purl.obolibrary.org/obo/GO_0045333 cellular respiration The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor. http://purl.obolibrary.org/obo/GO_0009273 peptidoglycan-based cell wall biogenesis http://purl.obolibrary.org/obo/GO_0042546 cell wall biogenesis The chemical reactions and pathways resulting in the formation of the peptidoglycan-based cell wall. An example of this process is found in Escherichia coli. [database_cross_reference: GOC:go_curators] http://purl.obolibrary.org/obo/GO_0009274 peptidoglycan-based cell wall http://purl.obolibrary.org/obo/GO_0005618 cell wall A protective structure outside the cytoplasmic membrane composed of peptidoglycan (also known as murein), a molecule made up of a glycan (sugar) backbone of repetitively alternating N-acetylglucosamine and N-acetylmuramic acid with short, attached, cross-linked peptide chains containing unusual amino acids. An example of this component is found in Escherichia coli. http://purl.obolibrary.org/obo/GO_0009275 Gram-positive-bacterium-type cell wall http://purl.obolibrary.org/obo/GO_0009274 peptidoglycan-based cell wall A layer of peptidoglycan found outside of the cytoplasmic membrane. The peptidoglycan is relatively thick (20-80nm) and retains the primary stain of the Gram procedure, thus cells appear blue after Gram stain. The cell walls often contain teichoic acids (acidic anionic polysaccharides) bound to the peptidoglycan. Examples of this component are found in Gram-positive bacteria. http://purl.obolibrary.org/obo/GO_0009276 Gram-negative-bacterium-type cell wall http://purl.obolibrary.org/obo/GO_0009274 peptidoglycan-based cell wall The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain. http://purl.obolibrary.org/obo/GO_0009288 bacterial-type flagellum http://purl.obolibrary.org/obo/GO_0043228 non-membrane-bounded organelle A motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. http://purl.obolibrary.org/obo/GO_0009289 pilus http://purl.obolibrary.org/obo/GO_0042995 cell projection A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter. http://purl.obolibrary.org/obo/GO_0009372 quorum sensing http://purl.obolibrary.org/obo/GO_0007267 cell-cell signaling The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms. http://purl.obolibrary.org/obo/GO_0009403 toxin biosynthetic process http://purl.obolibrary.org/obo/GO_0009404 toxin metabolic process The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/GO_0009404 toxin metabolic process http://purl.obolibrary.org/obo/GO_0008152 metabolic process The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. http://purl.obolibrary.org/obo/GO_0009405 pathogenesis http://purl.obolibrary.org/obo/BFO_0000015 process Process that generates the ability of a pathogen to induce disorder in an organism. http://purl.obolibrary.org/obo/GO_0009407 toxin catabolic process http://purl.obolibrary.org/obo/GO_0009404 toxin metabolic process The chemical reactions and pathways resulting in the breakdown of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism. [database_cross_reference: GOC:go_curators] http://purl.obolibrary.org/obo/GO_0009420 bacterial-type flagellum filament http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The long (approximately 20 nm), thin external structure of the bacterial-type flagellum, which acts as a propeller. http://purl.obolibrary.org/obo/GO_0009421 bacterial-type flagellum filament cap http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The proteinaceous structure at the distal tip of the bacterial-type flagellar filament. http://purl.obolibrary.org/obo/GO_0009422 bacterial-type flagellum hook-filament junction http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The region of the bacterial-type flagellum where the hook and filament meet. http://purl.obolibrary.org/obo/GO_0009424 bacterial-type flagellum hook http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The portion of the bacterial-type flagellum that connects the filament to the basal body. http://purl.obolibrary.org/obo/GO_0009425 bacterial-type flagellum basal body http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity One of the three major substructures of the bacterial-type flagellum, the basal body is embedded in the cell envelope (the plasma membrane, peptidoglycan cell wall, and, if one is present, the outer membrane); it houses the secretion apparatus that exports the more distal components and the flagellar motor. http://purl.obolibrary.org/obo/GO_0009426 bacterial-type flagellum basal body, distal rod http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The portion of the central rod of the bacterial-type flagellar basal body that is distal to the cell membrane; spans most of the distance between the inner and outer membranes. http://purl.obolibrary.org/obo/GO_0009427 bacterial-type flagellum basal body, distal rod, L ring http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the outer membrane. http://purl.obolibrary.org/obo/GO_0009428 bacterial-type flagellum basal body, distal rod, P ring http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity One of the rings of the bacterial-type flagellar basal body; anchors the basal body to the peptidoglycan layer. http://purl.obolibrary.org/obo/GO_0009429 bacterial-type flagellum basal body, proximal rod http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The portion of the central rod of the bacterial-type flagellar basal body that is proximal to the cell membrane; the proximal rod connects the distal rod to the flagellar motor. http://purl.obolibrary.org/obo/GO_0009431 bacterial-type flagellum basal body, MS ring http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity One of the rings of the bacterial-type flagellar basal body; a double-flanged ring that anchors the basal body to the cytoplasmic membrane. [database_cross_reference: GOC:cilia][database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192] http://purl.obolibrary.org/obo/GO_0009433 bacterial-type flagellum basal body, C ring http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity Cytoplasmic ring located at the base of the bacterial-type flagellar basal body; acts as a rotor; includes three switch proteins, which generate torque and can change their conformational state in a bimodal fashion, so that the motor direction can switch between clockwise and counterclockwise. [database_cross_reference: GOC:cilia][database_cross_reference: GOC:mtg_sensu][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192] http://purl.obolibrary.org/obo/GO_0009682 induced systemic resistance http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium A response to non-pathogenic bacteria that confers broad spectrum systemic resistance to disease that does not depend upon salicylic acid signaling. http://purl.obolibrary.org/obo/GO_0015159 polysaccharide transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0022857 transmembrane transporter activity Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. http://purl.obolibrary.org/obo/GO_0015161 capsular polysaccharide transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0015159 polysaccharide transmembrane transporter activity Enables the transfer of capsular-polysaccharides from one side of a membrane to the other. Capsular polysaccharides make up the capsule, a protective structure surrounding some species of bacteria and fungi. http://purl.obolibrary.org/obo/GO_0015267 channel activity http://purl.obolibrary.org/obo/GO_0022803 passive transmembrane transporter activity Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules. http://purl.obolibrary.org/obo/GO_0015774 polysaccharide transport http://purl.obolibrary.org/obo/GO_0006810 transport The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically. http://purl.obolibrary.org/obo/GO_0015776 capsular polysaccharide transport http://purl.obolibrary.org/obo/GO_0015774 polysaccharide transport The directed movement of capsular polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Capsular polysaccharides make up the capsule, a protective structure surrounding some species of bacteria and fungi. http://purl.obolibrary.org/obo/GO_0019867 outer membrane http://purl.obolibrary.org/obo/GO_0016020 membrane The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites. http://purl.obolibrary.org/obo/GO_0022803 passive transmembrane transporter activity http://purl.obolibrary.org/obo/GO_0022857 transmembrane transporter activity Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged. http://purl.obolibrary.org/obo/GO_0030198 extracellular matrix organization http://purl.obolibrary.org/obo/GO_0009987 cellular process A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix. http://purl.obolibrary.org/obo/GO_0030313 cell envelope http://purl.obolibrary.org/obo/GO_0031975 envelope An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present. http://purl.obolibrary.org/obo/GO_0030694 bacterial-type flagellum basal body, rod http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The central portion of the bacterial-type flagellar basal body, which spans the periplasm and threads through the rings. http://purl.obolibrary.org/obo/GO_0031224 intrinsic component of membrane http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The component of a membrane consisting of the gene products having some covalently attached portion, for example part of a peptide sequence or some other covalently attached group such as a GPI anchor, which spans or is embedded in one or both leaflets of the membrane. http://purl.obolibrary.org/obo/GO_0031982 vesicle http://purl.obolibrary.org/obo/GO_0043227 membrane-bounded organelle Any small, fluid-filled, spherical organelle enclosed by membrane. http://purl.obolibrary.org/obo/GO_0042742 defense response to bacterium http://purl.obolibrary.org/obo/GO_0006952 defense response Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism. http://purl.obolibrary.org/obo/GO_0043228 non-membrane-bounded organelle http://purl.obolibrary.org/obo/GO_0043226 organelle Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. http://purl.obolibrary.org/obo/GO_0044085 cellular component biogenesis http://purl.obolibrary.org/obo/GO_0071840 cellular component organization or biogenesis A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. [database_cross_reference: GOC:jl][database_cross_reference: GOC:mah] http://purl.obolibrary.org/obo/GO_0044403 symbiotic process http://purl.obolibrary.org/obo/GO_0008150 biological process Process carried out by gene products in an organism or acellular structure that enables the entity to engage in a symbiotic relationship with an organism. http://purl.obolibrary.org/obo/GO_0045333 cellular respiration http://purl.obolibrary.org/obo/GO_0009987 cellular process The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration). http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport http://purl.obolibrary.org/obo/GO_0015031 protein transport The process in which a protein is transported across a membrane. [database_cross_reference: GOC:mah][database_cross_reference: GOC:vw] http://purl.obolibrary.org/obo/GO_0071840 cellular component organization or biogenesis http://purl.obolibrary.org/obo/GO_0009987 cellular process A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component. [ GOC:mah ] http://purl.obolibrary.org/obo/GO_0098776 protein transport across the cell outer membrane http://purl.obolibrary.org/obo/GO_0071806 protein transmembrane transport The directed movement of proteins across the cell outer membrane. [database_cross_reference: GOC:dos] http://purl.obolibrary.org/obo/GO_0052001 type IV pili-dependent localized adherence to host http://purl.obolibrary.org/obo/GO_0044406 adhesion of symbiont to host Attachment of bacterial clusters to the surface of the host in a type IV pili dependent manner. The host is defined as the larger of the organisms involved in a symbiotic interaction. [database_cross_reference: GOC:ml] http://purl.obolibrary.org/obo/GO_0055040 periplasmic flagellum http://purl.obolibrary.org/obo/GO_0009288 bacterial-type flagellum Flagellar filaments located in the periplasmic space; characterized in spirochetes, in which they are essential for shape and motility. Composed of a core surrounded by two sheath layers, the flagella rotate to allow migration of the cell through viscous media, which would not be possible using external flagella. http://purl.obolibrary.org/obo/GO_0061701 bacterial outer membrane vesicle http://purl.obolibrary.org/obo/GO_1903561 extracellular vesicle A spherical, bilayered proteolipid vesicle released from gram-negative bacterial outer membranes. [database_cross_reference: GOC:dph][database_cross_reference: GOC:pr][database_cross_reference: PMID:20596524] http://purl.obolibrary.org/obo/GO_0070701 mucus layer http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity An extracellular region part that consists of a protective layer of mucus secreted by epithelial cells lining tubular organs of the body such as the colon or secreted into fluids such as saliva. Mucus is a viscous slimy secretion consisting of mucins (i.e. highly glycosylated mucin proteins) and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. [database_cross_reference: GOC:krc][database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394][database_cross_reference: Wikipedia:Mucin] http://purl.obolibrary.org/obo/GO_0070702 inner mucus layer http://purl.obolibrary.org/obo/GO_0070701 mucus layer The inner of two mucus layers secreted by epithelial cells in the colon; the inner mucus layer is firmly attached to the epithelium, is densely packed with a compact stratified appearance and is devoid of bacteria. [database_cross_reference: GOC:mah][database_cross_reference: GOC:mm2][database_cross_reference: PMID:18806221][database_cross_reference: PMID:19432394] http://purl.obolibrary.org/obo/GO_0071736 IgG immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0071739 IgD immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0071743 IgE immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0071746 IgA immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph. http://purl.obolibrary.org/obo/GO_0071754 IgM immunoglobulin complex, circulating http://purl.obolibrary.org/obo/GO_0042571 immunoglobulin complex, circulating A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph. http://purl.obolibrary.org/obo/GO_0071766 Actinobacterium-type cell wall biogenesis http://purl.obolibrary.org/obo/GO_0009273 peptidoglycan-based cell wall biogenesis A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cell wall of the type found in Actinobacteria. The cell wall is the rigid or semi-rigid envelope lying outside the cell membrane. Actinobacterial cell walls contain characteristic mycolic acids, of which some are covalently linked to the cell wall peptidoglycan and others accumulate at the cell surface. [database_cross_reference: GOC:mah][database_cross_reference: PMID:15653820][database_cross_reference: PMID:3149973] http://purl.obolibrary.org/obo/GO_0071973 bacterial-type flagellum-dependent cell motility http://purl.obolibrary.org/obo/GO_0097588 archaeal or bacterial-type flagellum-dependent cell motility Cell motility due to the motion of one or more bacterial-type flagella. A bacterial-type flagellum is a motor complex composed of an extracellular helical protein filament coupled to a rotary motor embedded in the cell envelope. http://purl.obolibrary.org/obo/GO_0071977 bacterial-type flagellum-dependent swimming motility http://purl.obolibrary.org/obo/GO_0071973 bacterial-type flagellum-dependent cell motility Bacterial-type flagellum-dependent cell motility that results in the smooth movement of a cell through a liquid medium. http://purl.obolibrary.org/obo/GO_0071978 bacterial-type flagellum-dependent swarming motility http://purl.obolibrary.org/obo/GO_0071973 bacterial-type flagellum-dependent cell motility Bacterial-type flagellum-dependent cell motility in which the action of numerous flagella results in the smooth movement of a group of cells along a solid surface. Swarming motility is observed in groups of bacteria. http://purl.obolibrary.org/obo/GO_0075325 spore dispersal http://purl.obolibrary.org/obo/GO_0000003 reproduction Any process in which an organism disseminates its spores. [database_cross_reference: Wikipedia:Spore] http://purl.obolibrary.org/obo/GO_0097588 archaeal or bacterial-type flagellum-dependent cell motility http://purl.obolibrary.org/obo/GO_0001539 cilium or flagellum-dependent cell motility Cell motility due to movement of bacterial- or archaeal-type flagella. http://purl.obolibrary.org/obo/CL_0001065 innate lymphoid cell http://purl.obolibrary.org/obo/CL_0000542 lymphocyte A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. http://purl.obolibrary.org/obo/OHMI_0000003 microbiome http://purl.obolibrary.org/obo/ENVO_00000428 biome A biome that consists of a collection of microorganisms (i.e., microbiota) and the surrounding environment where the microorganisms reside. http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity part of or substance produced by a multicellular organism with granularity above the level of a protein complex. http://purl.obolibrary.org/obo/IDO_0000400 symbiont role http://purl.obolibrary.org/obo/BFO_0000023 role A role borne by an organism in symbiosis. http://purl.obolibrary.org/obo/IDO_0000401 mutualist role http://purl.obolibrary.org/obo/IDO_0000400 symbiont role Symbiont role borne by an organism in which both symbionts derive a growth, survival, or fitness advantage from symbiosis. http://purl.obolibrary.org/obo/IDO_0000402 commensal role http://purl.obolibrary.org/obo/IDO_0000400 symbiont role Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis, while the other symbiont is neither advantaged nor disadvantaged. http://purl.obolibrary.org/obo/IDO_0000403 parasite role http://purl.obolibrary.org/obo/IDO_0000400 symbiont role Symbiont role borne by an organism that derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced. http://purl.obolibrary.org/obo/IDO_0000406 opportunistic infectious disposition http://purl.obolibrary.org/obo/ido.owl/IDO_0001157 infectious disposition Infectious disposition to become part of a disorder only in organisms whose defenses are compromised. http://purl.obolibrary.org/obo/IDO_0000409 definitive host role http://purl.obolibrary.org/obo/IDO_0000408 symbiont host role Symbiont host role borne by an organism whose partner in symbiosis reaches developmental maturity or reproduces sexually in the host. http://purl.obolibrary.org/obo/IDO_0000410 intermediate host role http://purl.obolibrary.org/obo/IDO_0000408 symbiont host role Symbiont host role borne by an organism whose partner in symbiosis utilizes the host to undergo a developmental stage transition, and the host is required for continuation of the partner's life cycle. http://purl.obolibrary.org/obo/IDO_0000412 dead-end host role http://purl.obolibrary.org/obo/IDO_0000408 symbiont host role Symbiont host role borne by an organism whose partner in symbiosis has the infectious disposition but cannot be transmitted from the host to the partner's definitive host. http://purl.obolibrary.org/obo/IDO_0000419 mechanical vector role http://purl.obolibrary.org/obo/ido.owl/IDO_0001130 pathogen vector role A pathogen vector role borne by an organism in virtue of the fact that the pathogen does not multiply in or on the vector. http://purl.obolibrary.org/obo/IDO_0000420 biological vector role http://purl.obolibrary.org/obo/ido.owl/IDO_0001130 pathogen vector role A pathogen vector role borne by an organism in virtue of the fact that the pathogen multiplies in the vector. http://purl.obolibrary.org/obo/IDO_0000421 pathogen vehicle role http://purl.obolibrary.org/obo/IDO_0001096 pathogen transporter role A pathogen transporter role borne by an entity in virtue of the fact that the entity is not a complete organism. http://purl.obolibrary.org/obo/IDO_0000422 biological vehicle role http://purl.obolibrary.org/obo/IDO_0000421 pathogen vehicle role A pathogen vehicle role borne by an entity in virtue of the fact that the entity is living or contains living cells other than those that have the infectious disposition. http://purl.obolibrary.org/obo/IDO_0000423 fomite role http://purl.obolibrary.org/obo/IDO_0000421 pathogen vehicle role An infectious agent vehicle role borne by an entity in virtue of the fact that the entity is not alive. http://purl.obolibrary.org/obo/IDO_0000427 exotoxin disposition http://purl.obolibrary.org/obo/IDO_0000426 toxin disposition Toxin disposition to damage cells or extracellular matrix by a direct enzymatic process. http://purl.obolibrary.org/obo/IDO_0000433 adhesion disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition borne by a macromolecule that is the disposition to participate in an adhesion process. http://purl.obolibrary.org/obo/IDO_0000434 primary infection role http://purl.obolibrary.org/obo/BFO_0000023 role Role borne by an infectious disorder whose host has another, distinct, infectious disorder - neither arising from the other through metastasis - which emerged after this infectious disorder was established due to increased host susceptibility to infectious disorders. http://purl.obolibrary.org/obo/IDO_0000435 secondary infection role http://purl.obolibrary.org/obo/BFO_0000023 role Role borne by an infectious disorder whose host has another, distinct, primary infectious disorder - neither arising from the other through metastasis - which emerged after the primary infectious disorder was established due to increased host susceptibility to infectious disorders. http://purl.obolibrary.org/obo/IDO_0000437 symbiont adhesion disposition http://purl.obolibrary.org/obo/IDO_0000433 adhesion disposition Disposition borne by a macromolecule part of a symbiont that is the disposition to participate in adherence to a host. http://purl.obolibrary.org/obo/IDO_0000446 resistance to pathogen http://purl.obolibrary.org/obo/IDO_0000444 protective resistance Protective resistance that inheres in an organism and mitigates the damaging effects of a pathogen. http://purl.obolibrary.org/obo/IDO_0000447 herd immunity to infectious pathogen http://purl.obolibrary.org/obo/IDO_0000588 collective resistance disposition Collective resistance disposition that inheres in an organism population where the proportion of the population with immunity to an infectious pathogen is high resulting in a low number of transmissions from hosts to susceptible individuals. http://purl.obolibrary.org/obo/IDO_0000448 immunity to pathogen http://purl.obolibrary.org/obo/IDO_0000446 resistance to pathogen Resistance to pathogen that inheres in an organism due to immune system components in its extended organism. http://purl.obolibrary.org/obo/IDO_0000449 sterilizing immunity to pathogen http://purl.obolibrary.org/obo/IDO_0000448 immunity to pathogen Immunity to pathogen that results in elimination of the pathogen from the host. http://purl.obolibrary.org/obo/IDO_0000451 invasive disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition borne by a pathogen that is the disposition to penetrate the epithelial barriers of an organism of another species. http://purl.obolibrary.org/obo/IDO_0000453 zoonotic disposition http://purl.obolibrary.org/obo/ido.owl/IDO_0001157 infectious disposition Infectious disposition to be transmitted from an infected, non-human host to a human host. http://purl.obolibrary.org/obo/IDO_0000454 reverse zoonotic disposition http://purl.obolibrary.org/obo/ido.owl/IDO_0001157 infectious disposition Infectious disposition to be transmitted from an infected, human host to a non-human host. http://purl.obolibrary.org/obo/IDO_0000456 immunosuppressed organism http://purl.obolibrary.org/obo/OBI_0100026 organism Organism that is experiencing immunosuppression. http://purl.obolibrary.org/obo/IDO_0000463 infectious pathogen transmissibility http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an infectious agent or infectious structure and is the likelihood that the agent or structure will undergo a horizontal transmission process. http://purl.obolibrary.org/obo/IDO_0000464 infectivity http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in a pathogen and is the likelihood that the infectious disposition will be realized upon exposure of a susceptible organism. http://purl.obolibrary.org/obo/IDO_0000466 virulence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in a pathogen and is the degree to which realizations of the infectious disease caused by the pathogen become severe or fatal. http://purl.obolibrary.org/obo/IDO_0000467 susceptibility http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an entity and is the degree to which it can be harmed by another entity. http://purl.obolibrary.org/obo/IDO_0000468 susceptibility to pathogen http://purl.obolibrary.org/obo/IDO_0000467 susceptibility Susceptibility that inheres in an organism and is the degree to which it can be harmed by a pathogen. http://purl.obolibrary.org/obo/IDO_0000469 drug susceptibility http://purl.obolibrary.org/obo/IDO_0000467 susceptibility Susceptibility that is the degree to which an entity can be harmed or inhibited from surviving by a drug. http://purl.obolibrary.org/obo/IDO_0000470 drug susceptibility of infectious pathogen http://purl.obolibrary.org/obo/IDO_0000469 drug susceptibility Drug susceptibility that inheres in an infectious pathogen and is the degree to which the infectious pathogen can be harmed or inhibited from surviving by a drug. http://purl.obolibrary.org/obo/IDO_0000471 complex infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection comprised of infectious organisms from different species. http://purl.obolibrary.org/obo/IDO_0000473 intracellular infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection in which pathogen parts persist inside host cells. http://purl.obolibrary.org/obo/IDO_0000474 systematic infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection for which the infectious agents or structures that are part of the infection are distributed throughout the host. http://purl.obolibrary.org/obo/IDO_0000475 local infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection for which the infectious agents or structures that are part of the infection are limited to a relatively small area of the host's body. http://purl.obolibrary.org/obo/IDO_0000477 acute infectious disease course http://purl.obolibrary.org/obo/IDO_0000495 infectious disease course Infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. http://purl.obolibrary.org/obo/IDO_0000479 infectious disease incidence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of realizations of an infectious disease for which the infectious disease course begins during a specified period of time. http://purl.obolibrary.org/obo/IDO_0000480 infection incidence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of organisms in the population that become infected with a pathogen during a specified period of time. http://purl.obolibrary.org/obo/IDO_0000483 infectious disease incidence rate http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the infectious disease incidence proportion per unit time. http://purl.obolibrary.org/obo/IDO_0000484 infection incidence rate http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the infection incidence proportion per unit time. http://purl.obolibrary.org/obo/IDO_0000485 infectious disease prevalence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of realizations of an infectious disease in the population at a specified time. http://purl.obolibrary.org/obo/IDO_0000486 infection prevalence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of organisms in the population infected with a pathogen at a specified time. http://purl.obolibrary.org/obo/IDO_0000487 infectious disease lifetime prevalence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of organisms in the population who have, at any point during their lives, been bearers of an infectious disease and experienced realization of the disease. http://purl.obolibrary.org/obo/IDO_0000488 pathogen seroprevalence http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the number of organisms in the population that have antibody specific for a pathogen in their serum at a specified time. http://purl.obolibrary.org/obo/IDO_0000489 infectious disease mortality rate http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population and is the per capita number of deaths in the population resulting from an infectious disease over a specified period of time. http://purl.obolibrary.org/obo/IDO_0000490 infectious disease endemicity http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population in virtue of the fact that infections of the type that causes an infectious disease are maintained in the population via intra-population transmission or by transmission from a local reservoir. http://purl.obolibrary.org/obo/IDO_0000493 infectious disease hyper-endemicity http://purl.obolibrary.org/obo/IDO_0000490 infectious disease endemicity An infectious disease endemicity that inheres in an organism population in virtue of the fact that the infectious disease endemic level for an infectious disease is persistently high in the population. http://purl.obolibrary.org/obo/IDO_0000494 infectious disease sporadicity http://purl.obolibrary.org/obo/BFO_0000019 quality Quality that inheres in an organism population by virtue of the fact that realizations of an infectious disease occur in the population with a fluctuating prevalence. http://purl.obolibrary.org/obo/IDO_0000496 long-term non-progressing infectious disease course http://purl.obolibrary.org/obo/IDO_0000590 chronic infectious disease course Chronic infectious disease course that does not progress to severe stages for a long period of time. http://purl.obolibrary.org/obo/IDO_0000497 immunization against pathogen http://purl.obolibrary.org/obo/BFO_0000015 process Process by which an organism acquires immunity to a pathogen. http://purl.obolibrary.org/obo/IDO_0000499 vaccination against pathogen http://purl.obolibrary.org/obo/IDO_0000498 active immunization against pathogen Active immunization that begins with exposure of an organism to a vaccine. http://purl.obolibrary.org/obo/IDO_0000500 variolation http://purl.obolibrary.org/obo/IDO_0000498 active immunization against pathogen Active immunization that begins with exposure to smallpox in the form of a scab from a pustule and results in immunity against smallpox. http://purl.obolibrary.org/obo/IDO_0000501 passive immunization against pathogen http://purl.obolibrary.org/obo/IDO_0000497 immunization against pathogen Immunization that begins with transfer to an organism of molecules not produced by that organism and that confer immunity against a pathogen. http://purl.obolibrary.org/obo/IDO_0000503 infectious disease pandemic http://purl.obolibrary.org/obo/BFO_0000015 process Process in which multiple infectious disease epidemics of the same type of infectious disease unfold over overlapping periods of time and affect organism populations located in different geographic regions, including different countries and continents. http://purl.obolibrary.org/obo/IDO_0000506 bacteremia http://purl.obolibrary.org/obo/IDO_0000472 extracellular infection Infection that has as part bacteria located in the blood. http://purl.obolibrary.org/obo/IDO_0000511 infected population http://purl.obolibrary.org/obo/IDO_0000509 organism population Organism population whose members have an infection. http://purl.obolibrary.org/obo/IDO_0000512 diseased population http://purl.obolibrary.org/obo/IDO_0000509 organism population Organism population in whose members an infectious disease is being realized. http://purl.obolibrary.org/obo/IDO_0000513 infectious agent population http://purl.obolibrary.org/obo/IDO_0000509 organism population Organism population whose members each have an infectious disposition. http://purl.obolibrary.org/obo/IDO_0000519 incubation interval http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region One-dimensional temporal region beginning with the establishment of an infectious agent or structure in a host and ending with the onset of symptoms in the host. http://purl.obolibrary.org/obo/IDO_0000520 communicability interval http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region One-dimensional temporal region during which a pathogen host bears a contagiousness disposition. http://purl.obolibrary.org/obo/IDO_0000523 obligatory symbiont http://purl.obolibrary.org/obo/IDO_0000522 symbiont Organism that can only reach developmental maturity, replicate, or persist in symbiosis. http://purl.obolibrary.org/obo/IDO_0000551 enterotoxin http://purl.obolibrary.org/obo/IDO_0000550 exotoxin Exotoxin bearing an enterotoxin disposition. http://purl.obolibrary.org/obo/IDO_0000552 endotoxin http://purl.obolibrary.org/obo/IDO_0000549 toxin Toxin bearing an endotoxin disposition that is a structural component of a pathogen and is released from the pathogen only upon cytolysis. http://purl.obolibrary.org/obo/IDO_0000554 pathogen portal of exit http://purl.obolibrary.org/obo/CARO_0000000 anatomical entity Anatomical entity bearing a pathogen portal of exit role. http://purl.obolibrary.org/obo/IDO_0000568 zoonosis http://purl.obolibrary.org/obo/IDO_0000436 infectious disease Infectious disease inhering in an infectious disorder composed of pathogens having zoonotic dispositions. http://purl.obolibrary.org/obo/IDO_0000571 resistant entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity bearing protective resistance. http://purl.obolibrary.org/obo/IDO_0000579 leukocyte-mediated immunity to pathogen http://purl.obolibrary.org/obo/IDO_0000448 immunity to pathogen Immunity to pathogen that inheres in an organism in virtue of its leukocytes. http://purl.obolibrary.org/obo/IDO_0000580 passive immunity to pathogen http://purl.obolibrary.org/obo/IDO_0000448 immunity to pathogen Immunity to pathogen that inheres in an organism in virtue of antibodies not produced by that organism. http://purl.obolibrary.org/obo/IDO_0000583 emerging pathogen http://purl.obolibrary.org/obo/IDO_0000528 pathogen Pathogen whose infection incidence is increasing following its first introduction into a new host Species. http://purl.obolibrary.org/obo/IDO_0000584 cytotoxin http://purl.obolibrary.org/obo/IDO_0000549 toxin Toxin bearing a cytotoxin disposition. http://purl.obolibrary.org/obo/IDO_0000585 collective pathogenic disposition http://purl.obolibrary.org/obo/IDO_0000455 collective disposition Collective disposition to initiate processes that result in a disorder. http://purl.obolibrary.org/obo/IDO_0000587 genetic resistance to pathogen http://purl.obolibrary.org/obo/IDO_0000446 resistance to pathogen Resistance to pathogen that inheres in an organism due to an allele or combination of alleles in its genome. http://purl.obolibrary.org/obo/IDO_0000588 collective resistance disposition http://purl.obolibrary.org/obo/IDO_0000455 collective disposition Collective disposition the realization of which mitigates the damaging effects of some entity on members of the collection. http://purl.obolibrary.org/obo/IDO_0000590 chronic infectious disease course http://purl.obolibrary.org/obo/IDO_0000495 infectious disease course Infectious disease course that unfolds over a long period of time. http://purl.obolibrary.org/obo/IDO_0000592 immune population http://purl.obolibrary.org/obo/IDO_0000509 organism population Organism population whose members have acquired immunity to an infectious agent. http://purl.obolibrary.org/obo/IDO_0000593 transmission interval http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region One-dimensional temporal region during which a transmission process occurs. http://purl.obolibrary.org/obo/IDO_0000603 process of establishing an infection http://purl.obolibrary.org/obo/BFO_0000015 process Process by which an infectious agent or infectious structure, established in a host, becomes part of an infection in the host. http://purl.obolibrary.org/obo/IDO_0000604 colonization of host http://purl.obolibrary.org/obo/IDO_0000625 establishment of localization in host Establishment of localization in host process in which an organism establishes a colony in or on a host. http://purl.obolibrary.org/obo/IDO_0000606 establishment of a clinically abnormal colony http://purl.obolibrary.org/obo/IDO_0000604 colonization of host Colonization of host process that results in a clinically abnormal colony. http://purl.obolibrary.org/obo/IDO_0000607 production http://purl.obolibrary.org/obo/BFO_0000015 process Process in which an entity comes into being as a result of the process. http://purl.obolibrary.org/obo/IDO_0000608 replication http://purl.obolibrary.org/obo/IDO_0000607 production Production process in which a participant creates a copy of itself. http://purl.obolibrary.org/obo/IDO_0000610 immunosuppression http://purl.obolibrary.org/obo/BFO_0000015 process Process that attenuates an immune response. http://purl.obolibrary.org/obo/IDO_0000611 physiologic immunosuppression http://purl.obolibrary.org/obo/IDO_0000610 immunosuppression Immunosuppression which unfolds as part of the natural self-regulation of an immune response. http://purl.obolibrary.org/obo/IDO_0000612 pathologic immunosuppression http://purl.obolibrary.org/obo/IDO_0000610 immunosuppression Immunosuppression process which arises as the result of a disorder. http://purl.obolibrary.org/obo/IDO_0000615 colony http://purl.obolibrary.org/obo/IDO_0000509 organism population Organism population persisting in a site it has colonized. http://purl.obolibrary.org/obo/IDO_0000616 infectious agent colony http://purl.obolibrary.org/obo/IDO_0000615 colony Colony whose members are infectious agents. http://purl.obolibrary.org/obo/IDO_0000617 immunodeficiency http://purl.obolibrary.org/obo/OGMS_0000045 disorder Disorder of an immune system component that results in defective functioning of the immune system. http://purl.obolibrary.org/obo/IDO_0000625 establishment of localization in host http://purl.obolibrary.org/obo/GO_0051234 establishment of localization Process in which a material entity reaches a site in or on a host in which it can survive, grow, multiply, or mature and establishes itself there. http://purl.obolibrary.org/obo/IDO_0000628 chronic infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection that persists for an extended period of time. http://purl.obolibrary.org/obo/IDO_0000631 community-acquired infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection resulting from a transmission process that did not unfold in a health care facility. http://purl.obolibrary.org/obo/IDO_0000632 neurotoxin http://purl.obolibrary.org/obo/IDO_0000549 toxin Toxin bearing a neurotoxin disposition. http://purl.obolibrary.org/obo/IDO_0000633 metastatic infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection established as a result of spread from another infection in a non-adjacent location in the extended organism of the host. http://purl.obolibrary.org/obo/IDO_0000635 source of infection role http://purl.obolibrary.org/obo/BFO_0000023 role Role borne by a material entity that contains a site from which an infectious agent is transmitted. http://purl.obolibrary.org/obo/IDO_0000638 nursing-home acquired infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection resulting from a transmission process that unfolds in a nursing home. http://purl.obolibrary.org/obo/IDO_0000639 infectious human pathogen http://purl.obolibrary.org/obo/IDO_0000528 pathogen Pathogen with a human infectious disposition. http://purl.obolibrary.org/obo/IDO_0000640 acquired immunodeficiency http://purl.obolibrary.org/obo/IDO_0000617 immunodeficiency Immunodeficiency that is not caused by a genetic predisposition. http://purl.obolibrary.org/obo/IDO_0000642 simple infection http://purl.obolibrary.org/obo/IDO_0000586 infection Infection comprised of infectious organisms or structures all of the same Species. http://purl.obolibrary.org/obo/IDO_0000643 re-emerging pathogen http://purl.obolibrary.org/obo/IDO_0000528 pathogen Pathogen whose infection incidence is increasing in a host population as a result of changes in the biology of the host or pathogen, or changes in their interactions. http://purl.obolibrary.org/obo/IDO_0000650 colonization of human http://purl.obolibrary.org/obo/IDO_0000604 colonization of host Colonization of host in a human. http://purl.obolibrary.org/obo/IDO_0000653 reverse zoonosis http://purl.obolibrary.org/obo/IDO_0000436 infectious disease Infectious disease inhering in an infectious disorder composed of pathogens bearing reverse zoonotic dispositions. http://purl.obolibrary.org/obo/IDO_0000655 transmissibility disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition Disposition to undergo a transmission process. http://purl.obolibrary.org/obo/IDO_0000656 horizontal pathogen transmission process http://purl.obolibrary.org/obo/TRANS_0000000 pathogen transmission process Pathogen transmission process in which a pathogen is transmitted from one host to another of the same species, and the two hosts are not in a parent-child relationship. http://purl.obolibrary.org/obo/IDO_0000657 process that results in death http://purl.obolibrary.org/obo/BFO_0000015 process Process that results in death. http://purl.obolibrary.org/obo/IDO_0000659 susceptible organism http://purl.obolibrary.org/obo/OBI_0100026 organism Organism that is not infected with an infectious agent or structure and lacks protective immunity to the infectious agent or structure. http://purl.obolibrary.org/obo/IDO_0000662 life-sustaining process http://purl.obolibrary.org/obo/GO_0008150 biological process Process which is necessary for the survival of an organism. http://purl.obolibrary.org/obo/IDO_0000665 source of infection http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity bearing a source of infection role. http://purl.obolibrary.org/obo/OGMS_0000020 symptom http://purl.obolibrary.org/obo/BFO_0000015 process Process experienced by a patient which can only be experienced by the patient, that is hypothesized to be clinically relevant. http://purl.obolibrary.org/obo/OGMS_0000045 disorder http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity that is a clinically abnormal part of an extended organism. http://purl.obolibrary.org/obo/PR_000050032 immunoglobulin complex (human) http://purl.obolibrary.org/obo/GO_0019814 immunoglobulin complex An immunoglobulin complex whose components are encoded in the genome of human. http://purl.obolibrary.org/obo/IDO_0001124 asymptomatic carrier role http://purl.obolibrary.org/obo/IDO_0000415 pathogen host role Pathogen host role borne by an organism whose extended organism contains a pathogen bearing an infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the pathogen. http://purl.obolibrary.org/obo/IDO_0001343 latency interval http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region One-dimensional temporal region beginning with the establishing of an infection in a host and ending when the host becomes contagious. http://purl.obolibrary.org/obo/ENVO_00000428 biome http://purl.obolibrary.org/obo/ENVO_01001110 ecosystem A biome is an ecosystem to which resident ecological communities have evolved adaptations. http://purl.obolibrary.org/obo/ENVO_00002034 biofilm http://purl.obolibrary.org/obo/BFO_0000027 object aggregate A complex aggregation of microorganisms marked by the excretion of a protective and adhesive matrix; usually adhering to a substratum. http://purl.obolibrary.org/obo/ERO_0000008 antibody reagent http://purl.obolibrary.org/obo/ERO_0000006 reagent A reagent that is comprised of immunoglobulins produced by B cells in response to an antigen. Antibody reagents can be engineered to have specificity for specific antigens. http://purl.obolibrary.org/obo/ERO_0000229 monoclonal antibody reagent http://purl.obolibrary.org/obo/ERO_0000008 antibody reagent Antibody reagent that recognizes a single epitope. http://purl.obolibrary.org/obo/ERO_0000347 intervention http://purl.obolibrary.org/obo/OBI_0000011 planned process Planned process used to influence one or more factors in a research study, and the independent variable in an interventional study wherein the influence is measured or evaluated. http://purl.obolibrary.org/obo/FMA_85431 porin http://purl.obolibrary.org/obo/PR_000000001 protein Beta barrel membrane transport protein that acts as a diffusion channel for small molecules. [This is an external definition] http://purl.obolibrary.org/obo/IDO_0001096 pathogen transporter role http://purl.obolibrary.org/obo/BFO_0000023 role Role borne by a material entity in or on which a pathogen is located, from which the pathogen may be transmitted to a new host. http://purl.obolibrary.org/obo/IDO_0001393 infectious disease mesoendemicity http://purl.obolibrary.org/obo/IDO_0000490 infectious disease endemicity To do http://purl.obolibrary.org/obo/IDO_0001089 cidal agent http://purl.obolibrary.org/obo/BFO_0000040 material entity Material entity with a cidal agent disposition. http://purl.obolibrary.org/obo/IDO_0001065 acellular structure aggregate http://purl.obolibrary.org/obo/BFO_0000027 object aggregate Aggregate of acellular structures. http://purl.obolibrary.org/obo/IDO_0001377 pathogen surveillance http://purl.obolibrary.org/obo/OBI_0002897 surveillance process Surveillance process aiming to produce information about one or more pathogens, with the purpose of managing those pathogens. http://purl.obolibrary.org/obo/NCIT_C20466 chemokine http://purl.obolibrary.org/obo/PR_000000001 protein Chemokines constitute a superfamily of small (8-10 kDa), inducible, secreted, pro-inflammatory cytokines that are involved in a variety of immune and inflammatory responses as well as in viral infection. Chemokines act primarily as chemoattractants and activators of specific types of leukocytes. Some members of this family were initially identified on the basis of their biological activities (e.g., IL-8, GRO), others were discovered using subtractive hybridization (e.g., RANTES) or signal sequence trap (e.g., PBSF/SDF-1)11 cloning strategies. They attract and activate leukocytes and regulate diverse cellular systems and organs ranging from blood vessels to the central nervous system. http://purl.obolibrary.org/obo/GO_0120101 bacterial-type flagellum stator complex http://purl.obolibrary.org/obo/GO_0005887 integral component of plasma membrane A hetero-hexameric complex of 2 membrane proteins, A and B, with stoichiometry A4B2. The A and B proteins form a channel through which flow the ions that power the bacterial-type flagellum. They form the stator, or nonrotating portion, of the flagellum motor with the B protein apparently attached to the peptidoglycan cell wall. Examples include the H+ driven MotA-MotB stator complex of Escherichia coli and Salmonella enterica, and the Na+ driven PomA-PomB stator complex of Vibrio and Shewanella species. http://purl.obolibrary.org/obo/GO_0120102 bacterial-type flagellum secretion apparatus http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity A part of the bacterial-type flagellum that is located at the cytoplasmic side of the MS ring and composed of six membrane proteins (FlhA, FlhB, FliP, FliQ, FliR, and FliO, or orthologs thereof) and three soluble proteins (FliI, FliH, and FliJ, or orthologs thereof) in the cytoplasm. It is responsible for secretion of flagellar type III protein substrates, including the proteins of the flagellar rod, hook, and filament. [database_cross_reference: GOC:cilia][database_cross_reference: PMID:10572114][database_cross_reference: PMID:12624192][database_cross_reference: PMID:24697492][database_cross_reference: DOI:10.1002/9780470015902.a0000744.pub4][database_cross_reference: PMID:25251856] Annotations http://www.ontologyrepository.com/CommonCoreOntologies/DesignativeInformationContentEntity designative information content entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity Information Content Entity that consists of a set of symbols that denote some Entity. http://purl.obolibrary.org/obo/IDO_0001378 vector surveillance http://purl.obolibrary.org/obo/OBI_0002897 surveillance process Surveillance process aiming to produce information about changes in the geographical distribution and density of one or several pathogen vectors, with the purpose of facilitating appropriate and timely desisions regarding interventions. http://purl.obolibrary.org/obo/IDO_0001025 fungicidal disposition http://purl.obolibrary.org/obo/IDO_0001092 cidal agent disposition Disposition inhering in a material entity, that is realized in a process of killing fungi. http://purl.obolibrary.org/obo/GO_0120107 bacterial-type flagellum rotor complex http://purl.obolibrary.org/obo/GO_0110165 cellular anatomical entity The rotor complex of the bacterial-type flagellum consists of a membrane-anchored ring and the motor switch complex, which participates in the conversion of proton/Na+ energy into the mechanical work of rotation and controls the direction of flagellar rotation. http://purl.obolibrary.org/obo/IDO_0001345 latency end process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the end of a latency period. http://purl.obolibrary.org/obo/IDO_0001357 communicability end process boundary http://purl.obolibrary.org/obo/BFO_0000035 process boundary Process boundary marking the end of a communicability interval. http://purl.obolibrary.org/obo/IDO_0001165 endotoxin disposition http://purl.obolibrary.org/obo/IDO_0000426 toxin disposition Toxin disposition that is a structural component of a pathogen and is realized only during cytolsis. http://purl.obolibrary.org/obo/IDO_0001166 enterotoxin disposition http://purl.obolibrary.org/obo/IDO_0000427 exotoxin disposition Exotoxin disposition ithat is realized in a process of damaging intestinal mucosa cells. http://purl.obolibrary.org/obo/IDO_0001021 colony forming unit per 100 milliliter http://purl.obolibrary.org/obo/UO_0000212 colony forming unit per volume A colony forming unit count which is a count of viable bacterial numbers in 100 milliliters of liquid. http://purl.obolibrary.org/obo/ENVO_01001110 ecosystem http://purl.obolibrary.org/obo/ENVO_01000254 enviromental system An environmental system which includes both living and non-living components. http://purl.obolibrary.org/obo/OBI_0002897 surveillance process http://purl.obolibrary.org/obo/OBI_0000066 investigation An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. http://purl.obolibrary.org/obo/CHEBI_35740 liposaccharide http://purl.obolibrary.org/obo/CHEBI_18059 lipid http://purl.obolibrary.org/obo/CHEBI_22506 aminoglycan http://purl.obolibrary.org/obo/CHEBI_65212 polysaccharide derivative http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000011 spatiotemporal region http://purl.obolibrary.org/obo/BFO_0000003 occurrent http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000009 two-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000018 zero-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000026 one-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000028 three-dimensional spatial region http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000038 one-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000148 zero-dimensional temporal region http://purl.obolibrary.org/obo/BFO_0000008 temporal region http://purl.obolibrary.org/obo/BFO_0000182 history http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/OGMS_0000060 bodily process http://purl.obolibrary.org/obo/BFO_0000015 process http://purl.obolibrary.org/obo/BFO_0000034 function http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000016 disposition http://purl.obolibrary.org/obo/BFO_0000017 realizable entity http://purl.obolibrary.org/obo/BFO_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant http://purl.obolibrary.org/obo/BFO_0000027 object aggregate http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000030 object http://purl.obolibrary.org/obo/BFO_0000040 material entity http://purl.obolibrary.org/obo/BFO_0000006 spatial region http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/BFO_0000029 site http://purl.obolibrary.org/obo/BFO_0000141 immaterial entity http://purl.obolibrary.org/obo/IDO_0001001 infection incidence proportion profile http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/IDO_0001002 infection incidence rate profile http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/IDO_0001000 infection incidence profile http://purl.obolibrary.org/obo/BFO_0000144 process profile http://purl.obolibrary.org/obo/GENEPIO_0001626 environmental datum http://purl.obolibrary.org/obo/IAO_0000109 measurement datum http://purl.obolibrary.org/obo/NCBITaxon_2 bacterium http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2759 eukaryota http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/OMIT_0018973 adhesins, bacterial http://purl.obolibrary.org/obo/OMIT_0002801 bacterial outer membrane proteins http://purl.obolibrary.org/obo/OMIT_0022740 fimbriae proteins http://purl.obolibrary.org/obo/OMIT_0002801 bacterial outer membrane proteins http://purl.obolibrary.org/obo/CL_0000520 prokaryotic cell http://purl.obolibrary.org/obo/CL_0000003 native cell http://purl.obolibrary.org/obo/BIDO_0000760 gram positive bacterium http://purl.obolibrary.org/obo/NCBITaxon_2 bacterium http://purl.obolibrary.org/obo/BIDO_0000761 gram negative bacterium http://purl.obolibrary.org/obo/NCBITaxon_2 bacterium http://purl.obolibrary.org/obo/CHEBI_25903 peptide antibiotic http://purl.obolibrary.org/obo/CHEBI_16670 peptide http://purl.obolibrary.org/obo/GO_0050765 negative regulation of phagocytosis http://purl.obolibrary.org/obo/GO_0065007 biological regulation http://purl.bioontology.org/ontology/NCBITAXON/4751 fungi http://purl.obolibrary.org/obo/NCBITaxon_2759 eukaryota http://purl.obolibrary.org/obo/NCBITaxon_9606 homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_2759 eukaryota http://purl.obolibrary.org/obo/PR_000024938 interferon alpha http://purl.obolibrary.org/obo/PR_000025848 type I interferon http://purl.obolibrary.org/obo/PR_000024939 interferon beta http://purl.obolibrary.org/obo/PR_000025848 type I interferon http://purl.obolibrary.org/obo/OMIT_0002801 bacterial outer membrane proteins http://purl.obolibrary.org/obo/PR_000036195 bacterial protein http://purl.obolibrary.org/obo/GO_0015628 protein secretion by the type II secretion system http://purl.obolibrary.org/obo/GO_0098776 protein transport across the cell outer membrane http://purl.obolibrary.org/obo/GO_0009279 cell outer membrane bacterial outer membrane A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. http://purl.obolibrary.org/obo/IDO_0000450 pathogenic disposition pathogenicity Disposition borne by a material entity to establish localization in or produce toxins that can be transmitted to an organism or acellular structure, either or which may form disorder in the entity or immunocompetent members of the entity's species. http://purl.obolibrary.org/obo/IDO_0000530 primary pathogen principal pathogen Pathogen bearing a primary infectious disposition. http://purl.obolibrary.org/obo/IDO_0000532 definitive host primary host Host bearing a definitive host role. http://purl.obolibrary.org/obo/IDO_0000533 intermediate host secondary host Host bearing an intermediate host role. http://purl.obolibrary.org/obo/IDO_0000535 dead-end host incidental host Host bearing a dead-end host role. http://purl.obolibrary.org/obo/IDO_0000548 invasion factor invasin Biological macromolecule that has an invasion disposition. http://purl.obolibrary.org/obo/IDO_0000557 adhesion factor adhesion molecule Biological macromolecule that has an adhesion disposition. http://purl.obolibrary.org/obo/IDO_0000589 immunodeficient organism immunocompromised organism Organism that has an immunodeficiency. http://purl.obolibrary.org/obo/IDO_0000621 acquired immunity to pathogen adaptive immunity to infectious agent Immunity to pathogen that inheres in an organism in virtue of antigen receptors encoded by somatically diversified genes in the organism's genome and expressed by cells that have undergone selection during a primary immune response in that organism. http://purl.obolibrary.org/obo/IDO_0000630 hospital-acquired infection nosocomial infection Infection resulting from a transmission process that unfolds in a hospital. http://purl.obolibrary.org/obo/IDO_0000654 opportunistic pathogen opportunist Pathogen with an opportunistic infectious disposition. http://purl.obolibrary.org/obo/IDO_0001005 pathologically immunosuppressed organism Immunosuppressed organism that is experiencing pathologic immunosuppression. http://purl.obolibrary.org/obo/IDO_0001007 negative regulation of production Process that stops, prevents, or reduces the frequency, rate or extent of a production process. http://purl.obolibrary.org/obo/IDO_0001008 negative regulation of replication Process that stops, prevents, or reduces the frequency, rate or extent of a replication process. http://purl.obolibrary.org/obo/IDO_0001010 pathogen death process boundary Process boundary that marks the end of the life cycle of a pathogen. http://purl.obolibrary.org/obo/GO_0106234 outer membrane protein complex Any protein complex that is part of the bacterial outer membrane. An example In E.coli, is RcsF associated with any one of several outer membrane beta-barrel proteins (OMPs), such as OmpA, OmpF, or OmpcC. http://purl.obolibrary.org/obo/CHEBI_24432 biological role Role inhering in a molecular entity or part of that entity, realized in biological processes. http://purl.obolibrary.org/obo/APOLLO_SV_00000086 infectious disease control strategy Plan specification whose objective specification is an infectious disease control objective specification. http://purl.obolibrary.org/obo/IDO_0001054 infectious structure Acellular structure that has an infectious disposition. http://purl.obolibrary.org/obo/BIDO_0000600 bacterial infection Infection that has as part some bacterium. http://purl.obolibrary.org/obo/BIDO_0000603 bacterial infectious disease course Infectious disease course that is the realization of a bacterial infectious disease. http://purl.obolibrary.org/obo/BIDO_0000750 bactericidal antibiotic Antibiotic that is used to kill bacteria. http://purl.obolibrary.org/obo/BIDO_0000751 bacteriostatic antibiotic Antibiotic that is used to inhibit the growth of bacteria. http://purl.obolibrary.org/obo/BIDO_0000762 aerobic bacterium Bacterium that is capable of growing and surviving in an oxygenated environment. http://purl.obolibrary.org/obo/BIDO_0000763 obligate aerobe bacterium Aerobic bacterium that requires oxygen to survive and grow. http://purl.obolibrary.org/obo/BIDO_0000764 facultative anaerobe bacterium Anaerobic bacterium that is capable of anaerobic methods of energy production but uses aerobic respiration in the presence of oxygen. http://purl.obolibrary.org/obo/BIDO_0000765 anaerobic bacterium Bacterium that is capable of surviving and growing in the absence of oxygen. http://purl.obolibrary.org/obo/BIDO_0000766 obligate anaerobe bacterium Anaerobic bacterium that only uses anaerobic methods of energy production and is harmed by the presence of oxygen. http://purl.obolibrary.org/obo/BIDO_0000767 cocci bacterium Bacterium that has a spherical or oval shape. http://purl.obolibrary.org/obo/BIDO_0000768 bacilli bacterium Bacterium that is rod-shaped. http://purl.obolibrary.org/obo/BIDO_0000769 spirochetes bacterium Bacterium that is flexible and has a thin, elongated, spiral shape. http://purl.obolibrary.org/obo/BIDO_0000770 spirilla bacterium Bacterium that is rigid and has an elongated, spiral shape. http://purl.obolibrary.org/obo/BIDO_0000771 aerotolerant anaerobe bacterium Anaerobic bacterium that only uses fermentation for energy production but is unharmed by the presence of oxygen. http://purl.obolibrary.org/obo/BIDO_0000772 microaerophile bacterium Obligate aerobic bacterium that requires oxygen for energy production but is harmed in atmospheric concentrations of oxygen (21% O2). http://purl.obolibrary.org/obo/BIDO_0000774 bacteria colony Colony whose members are bacteria. http://purl.obolibrary.org/obo/BIDO_0000775 bacteria population Organism population whose members are bacteria. http://purl.obolibrary.org/obo/BIDO_0000776 bacteria host Host whose extended organism has some bacterium part. http://purl.obolibrary.org/obo/BIDO_0000777 appearance of bacterial infectious disorder Apperance of disorder by which a bacterial infectious disorder comes into existence. http://purl.obolibrary.org/obo/BIDO_0000778 process of establishing a bacterial infection Process of establishing an infection in which a bacterium participates. http://purl.obolibrary.org/obo/BIDO_0000780 bacterial pathogenesis involving an infection Bacterial pathogenesis having at least the proper process parts: (1) establishment of localization in host, (2) process of establishing a bacterial infection, and (3) appearance of bacterial infectious disorder. http://purl.obolibrary.org/obo/BIDO_0000788 bacterial adhesion disposition Adhesion disposition borne by a macromolecule that is part of some bacterium that is the disposition to participate in the adhesion of the bacterium to a host. http://purl.obolibrary.org/obo/BIDO_0000800 bacterial biofilm Biofilm consisting of an aggregate of surface-associated bacteria that are enveloped in a biofilm matrix produced by those bacteria. http://purl.obolibrary.org/obo/BIDO_0000801 bacterial adhesion factor Adhesion factor that is part of some bacterium. http://purl.obolibrary.org/obo/IDO_0001396 immunological memory disposition Collective disposition inhering in some population of memory B cells and memory T cells, that is the ability of the immune system to quickly recognize a previously encountered antigen and to initiate a quicker and quantitatively better secondary immune response upon subsequent exposures to that same antigen. http://purl.obolibrary.org/obo/IDO_0000586 infection Material entity that is part of an extended organism that has some pathogen as part, which participates in the formation of the material entity by invading tissues of the organism. http://purl.obolibrary.org/obo/OBI_0000047 processed material Material entity that is created or changed during material processing. http://purl.obolibrary.org/obo/OBI_0001714 B cell epitope specific immunoglobulin-mediated neutralization immunoglobulin-mediated neutralization resulting from antibody binding to epitope http://purl.obolibrary.org/obo/OBI_1110001 epitope Material entity entity bearing the epitope role. http://purl.obolibrary.org/obo/CL_0001067 group 1 innate lymphoid cell An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. http://purl.obolibrary.org/obo/IDO_0001127 asymptomatic infectious structure carrier Infectious structure host bearing an asymptomatic carrier role. http://purl.obolibrary.org/obo/IDO_0001349 infection end temporal region Zero-dimensional temporal region occupied by an infection end process boundary. http://purl.obolibrary.org/obo/CL_0000219 motile cell A cell that moves by its own activities. http://purl.obolibrary.org/obo/CL_0000910 cytotoxic T cell A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. http://purl.obolibrary.org/obo/CL_0000912 helper T cell A effector T cell that provides help in the form of secreted cytokines to other immune cells. http://purl.obolibrary.org/obo/CL_0000946 antibody secreting cell A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. http://purl.obolibrary.org/obo/IDO_0001041 bactericidal Cidal agent with a bactericidal disposition. http://purl.obolibrary.org/obo/IDO_0001196 pathogen vector Pathogen transporter bearing a pathogen vector role. http://purl.obolibrary.org/obo/IDO_0001350 latency end temporal region Zero-dimensional temporal region occupied by a latency end process boundary. http://purl.obolibrary.org/obo/ido.owl/IDO_0001072 site of infection Anatomical space in which an infection is located. http://purl.obolibrary.org/obo/ido.owl/IDO_0001157 infectious disposition Pathogenic disposition borne by a pathogen to be transmitted to a host and then become part of an infection in that host or immunocompetent members of the same species as the host. http://purl.obolibrary.org/obo/CMO_0002652 bacterial infection severity measurement Any measurement of the degree to which the presentation of a bacterial infection has caused pain or damage, or of the degree to which bacteria has established lesions or infectious colonies, and/or taken over or interfered with the normal functioning of the body as a whole, or of one or more organs, tissues, cells or subcellular mechanisms of an organism. http://purl.obolibrary.org/obo/DRON_00000005 drug product A material entity (1) containing at least one scattered molecular aggregate as part that is the bearer of an active ingredient role and (2) that is itself the bearer of a clinical drug role http://purl.obolibrary.org/obo/DRON_00000030 role of scattered molecular aggregate A role borne by a scattered molecular aggregate and realized by its grains participating in one or more processes http://purl.obolibrary.org/obo/DRON_00000031 drug administration A treatment that has as participants an extended organism and a drug product and that results in part of the drug product being located in the extended organism http://purl.obolibrary.org/obo/IDO_0000444 protective resistance Disposition inhering in an acellular structure or organism, with a part having a disposition to mitigate damage to the entity from invasive or internal threats, which is realized in one or more negative biological regulation process. http://purl.obolibrary.org/obo/IDO_0000531 host Object bearing a host role. http://purl.obolibrary.org/obo/IDO_0001397 latent infection Infection for which the infectious agents or structures that are part of the infection are not multiplying in the host. http://purl.obolibrary.org/obo/IDO_0001351 communicability end temporal region Zero-dimensional temporal region occupied by a communicability end process boundary. http://purl.obolibrary.org/obo/GO_0002286 T cell activation involved in immune response The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/GO_0002292 T cell differentiation involved in immune response The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells. [database_cross_reference: GOC:add][database_cross_reference: ISBN:0781735149] http://purl.obolibrary.org/obo/GO_0002309 T cell proliferation involved in immune response The expansion of a T cell population by cell division as part of an immune response. [database_cross_reference: ISBN:0781735149][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/GO_0002312 B cell activation involved in immune response The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/GO_0002313 mature B cell differentiation involved in immune response The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/GO_0002322 B cell proliferation involved in immune response The expansion of a B cell population by cell division following B cell activation during an immune response. [database_cross_reference: GOC:jal] http://purl.obolibrary.org/obo/GO_0002323 natural killer cell activation involved in immune response The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response. [database_cross_reference: PMID:15032583][database_cross_reference: GOC:add] http://purl.obolibrary.org/obo/GO_0002325 natural killer cell differentiation involved in immune response The process in which a naive natural killer cell acquires the specialized features of an effector natural killer T cell as part of an immune response. [database_cross_reference: GOC:add][database_cross_reference: PMID:11698225] http://purl.obolibrary.org/obo/GO_0002367 cytokine production involved in immune response The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels. http://purl.obolibrary.org/obo/GO_0022402 cell cycle process The cellular process that ensures successive accurate and complete genome replication and chromosome segregation. [database_cross_reference: GOC:isa_complete][database_cross_reference: GOC:mtg_cell_cycle] http://purl.obolibrary.org/obo/GO_0098796 membrane protein complex Any protein complex that is part of a membrane. http://purl.obolibrary.org/obo/GO_0098797 plasma membrane protein complex Any protein complex that is part of the plasma membrane. [database_cross_reference: GOC:dos] http://purl.obolibrary.org/obo/GO_0044409 entry into host Penetration by an organism, or acellular structure, into the body, tissues, or cells of the host organism. http://purl.obolibrary.org/obo/GO_0044786 cell cycle DNA replication The DNA-dependent DNA replication that takes place as part of the cell cycle. http://purl.obolibrary.org/obo/GO_2000535 regulation of entry of bacterium into host cell Any process that modulates the frequency, rate or extent of entry of bacterium into host cell. [database_cross_reference: GOC:obol] http://purl.obolibrary.org/obo/GO_2000536 negative regulation of entry of bacterium into host cell Any process that stops, prevents or reduces the frequency, rate or extent of entry of bacterium into host cell. [database_cross_reference: GOC:obol] http://purl.obolibrary.org/obo/GO_1903561 extracellular vesicle Any vesicle that is part of the extracellular region. http://purl.obolibrary.org/obo/IDO_0001085 pathogen death temporal region Zero-dimensional temporal region occupied by a pathogen death process boundary. http://purl.obolibrary.org/obo/IDO_0001093 infectious structure host Pathogen host bearing an infectious structure host role. http://purl.obolibrary.org/obo/IDO_0001167 symptomatic infectious structure carrier Infectious structure host bearing a symptomatic carrier role. http://purl.obolibrary.org/obo/IDO_0001094 infectious structure host role Pathogen host role borne by an object or organism whose extended organism contains an infectious structure. http://purl.obolibrary.org/obo/IDO_0000407 primary infectious disposition Infectious disposition to become part of a disorder in immunocompetent organisms. http://purl.obolibrary.org/obo/IDO_0000408 symbiont host role Host role borne by an organism whose extended organism provides an environment supportive for the survival, growth, maturation, or reproduction of an object contained as a proper part. http://purl.obolibrary.org/obo/IDO_0000414 infectious agent host role Pathogen host role borne by an organism whose extended organism contains an infectious agent. http://purl.obolibrary.org/obo/IDO_0000415 pathogen host role Host role borne by an organism having a pathogen as part of its extended organism. http://purl.obolibrary.org/obo/IDO_0000424 reservoir of pathogen role Role borne by a material entity in which pathogens can persist, and from which they can be transmitted to hosts. http://purl.obolibrary.org/obo/IDO_0000425 virulence factor disposition Disposition borne by a biological macromolecule produced by a pathogen that is a disposition to undergo processes that increase the pathogen's virulence. http://purl.obolibrary.org/obo/IDO_0000426 toxin disposition Disposition to cause I) malfunction of cells, ii) damage to extracellular matrix, or iii) damage of cells to a degree that can result in cell death. http://purl.obolibrary.org/obo/IDO_0000430 pathogen portal of entry role Role borne by an anatomical entity that serves as the site through which a pathogen enters a host. http://purl.obolibrary.org/obo/IDO_0000431 pathogen portal of exit role Role borne by an anatomical entity that serves as the site through which a pathogen exits a host. http://purl.obolibrary.org/obo/IDO_0000455 collective disposition Disposition that inheres in a collection of entities in virtue of the individual dispositions of the constituents of that collection. http://purl.obolibrary.org/obo/IDO_0000457 immunocompetent organism Organism that has immunocompetence. http://purl.obolibrary.org/obo/IDO_0000458 contagiousness Disposition that inheres in a pathogen host and is a disposition to horizontally transmit that pathogen to organisms of the same species as the host, through casual contact, with a high likelihood of realization. http://purl.obolibrary.org/obo/IDO_0000459 colonized host Host that contains a colony in or on its extended organism. http://purl.obolibrary.org/obo/IDO_0000472 extracellular infection Infection in which pathogen parts persist in the extracellular space of the host. http://purl.obolibrary.org/obo/IDO_0000495 infectious disease course Disease course that is the realization of an infectious disease. http://purl.obolibrary.org/obo/IDO_0000504 infectious disorder Disorder that is part of an extended organism which has an infectious pathogen part, that exists as a result of a process of formation of disorder initiated by the infectious pathogen. http://purl.obolibrary.org/obo/IDO_0000522 symbiont Organism bearing a symbiont role. http://purl.obolibrary.org/obo/IDO_0000524 mutualist Symbiont bearing a mutualist role. http://purl.obolibrary.org/obo/IDO_0000525 commensal Symbiont bearing a commensal role. http://purl.obolibrary.org/obo/IDO_0000526 parasite Symbiont bearing a parasite role. http://purl.obolibrary.org/obo/IDO_0000528 pathogen Material entity bearing a pathogenic disposition. http://purl.obolibrary.org/obo/IDO_0000537 infectious agent host Pathogen host bearing an infectious agent host role. http://purl.obolibrary.org/obo/IDO_0000538 pathogen host Host bearing a pathogen host role. http://purl.obolibrary.org/obo/IDO_0000539 asymptomatic infectious agent carrier Infectious agent host bearing the infectious agent carrier role. http://purl.obolibrary.org/obo/IDO_0000543 pathogen vehicle Pathogen transporter bearing a pathogen vehicle role. http://purl.obolibrary.org/obo/IDO_0000544 fomite Pathogen vehicle bearing a fomite role. http://purl.obolibrary.org/obo/IDO_0000545 pathogen reservoir Material entity bearing a pathogen reservoir role. http://purl.obolibrary.org/obo/IDO_0000547 virulence factor A macromolecule produced by a pathogen and that has a virulence factor disposition. http://purl.obolibrary.org/obo/IDO_0000549 toxin Molecular entity that has a toxin disposition. http://purl.obolibrary.org/obo/IDO_0000550 exotoxin Toxin bearing an exotoxin disposition. http://purl.obolibrary.org/obo/IDO_0000553 pathogen portal of entry Anatomical entity bearing a pathogen portal of entry role. http://purl.obolibrary.org/obo/IDO_0000566 primary infection Infectious disorder bearing a primary infection role. http://purl.obolibrary.org/obo/IDO_0000567 secondary infection Infectious disorder bearing a secondary infection role. http://purl.obolibrary.org/obo/IDO_0000570 subclinical infection Infection that is part of an asymptomatic carrier. http://purl.obolibrary.org/obo/IDO_0000576 innate immunity to pathogen Immunity to pathogen that inheres in an organism in virtue of germline encoded components that directly recognize components of potential pathogens. http://purl.obolibrary.org/obo/IDO_0000578 humoral immunity to pathogen Immunity to pathogen that inheres in an organism in virtue of components of its circulating body fluid, e.g. blood, lymph, hemolymph. http://purl.obolibrary.org/obo/IDO_0000596 infectious agent Organism that has an infectious disposition. http://purl.obolibrary.org/obo/IDO_0000618 immunocompetence Disposition inhering in an organism that is the disposition to mount a normal immune response. http://purl.obolibrary.org/obo/IDO_0000619 immunosuppressive disposition Disposition whose realization negatively regulates an immune response. http://purl.obolibrary.org/obo/IDO_0000623 communicability Infectious disposition to be transmitted from one organism to another of the same species by horizontal transmission. http://purl.obolibrary.org/obo/IDO_0000626 appearance of disorder Process by which a disorder comes into existence. http://purl.obolibrary.org/obo/IDO_0000627 acute infection Infectious disorder that is the physical basis for an unfolding acute infectious disease course. http://purl.obolibrary.org/obo/IDO_0000663 negative regulation of life-sustaining process Process that stops, prevents, or reduces the frequency, rate or extent of a life-sustaining process. http://purl.obolibrary.org/obo/IDO_0001394 hospitalized host Host that has been hospitalized. http://purl.obolibrary.org/obo/ERO_0000006 reagent Processed material bearing a reagent role. http://purl.obolibrary.org/obo/IDO_0001352 incubation end temporal region Zero-dimensional temporal region occupied by an incubation end process boundary. http://purl.obolibrary.org/obo/IDO_0001353 communicability start temporal region Zero-dimensional temporal region occupied by a communicability start process boundary. http://purl.obolibrary.org/obo/IDO_0001198 mechanical vector Pathogen vector bearing a mechanical vector role. http://purl.obolibrary.org/obo/IDO_0001095 pathogen transporter Material entity bearing a pathogen transporter role. http://purl.obolibrary.org/obo/IDO_0001126 asymptomatic carrier Pathogen host with an infection as part bearing an asymptomatic carrier role. http://purl.obolibrary.org/obo/IDO_0001027 bactericidal disposition Disposition inhering in a material entity, that is realized in a process of killing bacteria. http://purl.obolibrary.org/obo/IDO_0001199 biological vehicle Pathogen vehicle bearing a biological vehicle role. http://purl.obolibrary.org/obo/IDO_0001168 symptomatic infectious agent carrier Infectious agent host bearing an infectious agent carrier role. http://purl.obolibrary.org/obo/IDO_0001197 biological vector Pathogen vector bearing a biological vector role. http://purl.obolibrary.org/obo/IDO_0001134 symptomatic carrier Pathogen host with infection as part that exhibits symptoms. http://purl.obolibrary.org/obo/VO_0000165 bacterial vaccine A vaccine that targets against a bacterial disease. http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/GO_0002324 natural killer cell proliferation involved in immune response http://purl.obolibrary.org/obo/RO_0002234 has output http://purl.obolibrary.org/obo/RO_0000057 has participant produces p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. http://purl.obolibrary.org/obo/RO_0000079 function of http://purl.obolibrary.org/obo/RO_0000052 inheres in is function of a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000080 quality of http://purl.obolibrary.org/obo/RO_0000052 inheres in quality_of a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000085 has function http://purl.obolibrary.org/obo/RO_0000053 bearer of has_function a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000086 has quality http://purl.obolibrary.org/obo/RO_0000053 bearer of has_quality a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002350 member of http://purl.obolibrary.org/obo/BFO_0000050 part of member part of is member of is a mereological relation between a item and a collection. http://purl.obolibrary.org/obo/RO_0000087 has role http://purl.obolibrary.org/obo/RO_0000053 bearer of has_role a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000081 role of http://purl.obolibrary.org/obo/RO_0000052 inheres in role_of a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/OBI_0000295 is specified input of http://purl.obolibrary.org/obo/RO_0000056 participates in Participates in relation between a planned process and a continuant participating in that process that is not created during the process, where the presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_0000312 is specified output of http://purl.obolibrary.org/obo/RO_0000056 participates in Participates in relation between a planned process and a continuant participating in that process where the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. http://purl.obolibrary.org/obo/OBI_1110060 process is result of http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by Is a relationship between a process and a preceding occurrent that directly caused the later one to occur http://purl.obolibrary.org/obo/RO_0002351 has member http://purl.obolibrary.org/obo/BFO_0000051 has part has member is a mereological relation between a collection and an item. http://purl.obolibrary.org/obo/RO_0000091 has disposition http://purl.obolibrary.org/obo/RO_0000053 bearer of a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0002212 negatively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates x negatively regulates y if and only if the progression of x reduces the frequency, rate or extent of y http://purl.obolibrary.org/obo/RO_0002213 positively regulates http://purl.obolibrary.org/obo/RO_0002211 regulates x positively regulates y if and only if the progression of x increases the frequency, rate or extent of y http://purl.obolibrary.org/obo/RO_0002087 immediately preceded by http://purl.obolibrary.org/obo/BFO_0000062 preceded by starts_at_end_of http://purl.obolibrary.org/obo/RO_0002090 immediately precedes http://purl.obolibrary.org/obo/BFO_0000063 precedes meets http://purl.obolibrary.org/obo/RO_0000092 disposition of http://purl.obolibrary.org/obo/RO_0000052 inheres in http://purl.obolibrary.org/obo/OBI_0000293 has specified input http://purl.obolibrary.org/obo/RO_0000057 has participant http://purl.obolibrary.org/obo/OBI_0000299 has specified output http://purl.obolibrary.org/obo/RO_0000057 has participant http://purl.obolibrary.org/obo/IAO_0000039 has measurement unit label http://purl.obolibrary.org/obo/BFO_0000051 has part http://purl.obolibrary.org/obo/RO_0002297 results in formation of http://purl.obolibrary.org/obo/IDO_0000660 results in http://purl.obolibrary.org/obo/RO_0000052 inheres in inheres_in a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000053 bearer of is bearer of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence http://purl.obolibrary.org/obo/RO_0000056 participates in participates_in a relation between a continuant and a process, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0000057 has participant has_participant a relation between a process and a continuant, in which the continuant is somehow involved in the process http://purl.obolibrary.org/obo/RO_0001000 derives from derives_from a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001001 derives into derives_into a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity http://purl.obolibrary.org/obo/RO_0001015 location of location_of a relation between two independent continuants, the location and the target, in which the target is entirely within the location http://purl.obolibrary.org/obo/RO_0002000 2D boundary of is boundary of a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0002002 has 2D boundary has_2D_boundary a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity http://purl.obolibrary.org/obo/RO_0001025 located in located_in a relation between two independent continuants, the target and the location, in which the target is entirely within the location http://purl.obolibrary.org/obo/BFO_0000051 has part has_part a core relation that holds between a whole and its part http://purl.obolibrary.org/obo/BFO_0000050 part of part_of a core relation that holds between a part and its whole http://purl.obolibrary.org/obo/BFO_0000066 occurs in unfolds_in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/RO_0002215 capable of has function realized in A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. http://purl.obolibrary.org/obo/VO_0003355 immunizes against immunization against microbe a shortcut relation that equals to: processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE')))))))) The domain of this relation is a vaccine. The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite) http://purl.obolibrary.org/obo/RO_0002371 attached to A is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a http://purl.obolibrary.org/obo/BFO_0000067 contains process [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t http://purl.obolibrary.org/obo/IAO_0000136 is about A (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/OBI_1110119 bound_to A relationship between two material entities that form a complex based on a selective, non-covalent interaction. http://purl.obolibrary.org/obo/RO_0000058 is concretized as A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. http://purl.obolibrary.org/obo/RO_0000059 concretizes A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/RO_0003000 produces a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. http://purl.obolibrary.org/obo/RO_0002211 regulates x regulates y if and only if the x is the realization of a function to exert an effect on the frequency, rate or extent of y http://purl.obolibrary.org/obo/BFO_0000054 realized in realized_in http://purl.obolibrary.org/obo/BFO_0000062 preceded by preceded_by http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/BFO_0000063 precedes http://purl.obolibrary.org/obo/IDO_0000664 has_material_basis_in http://purl.obolibrary.org/obo/BFO_999999 occupies temporal region http://purl.obolibrary.org/obo/cl#lacks_part lacks_part http://purl.obolibrary.org/obo/IDO_0000660 results in http://www.obofoundry.org/ro/ro.owl#has_proper_part has_proper_part