Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/BFO_0000002 continuant http://purl.obolibrary.org/obo/BFO_0000001 entity endurant 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 perdurant An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. http://purl.obolibrary.org/obo/BFO_0000004 independent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant substantial entity 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_0000020 specifically dependent continuant http://purl.obolibrary.org/obo/BFO_0000005 dependent continuant trope A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. http://purl.obolibrary.org/obo/IAO_0000027 data item http://purl.obolibrary.org/obo/IAO_0000030 information content entity data a data item is 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/IAO_0000300 textual entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity text A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. http://purl.obolibrary.org/obo/OBI_0200000 data transformation http://purl.obolibrary.org/obo/OBI_0000011 planned process data processing A data transformation is a process which produces output data from input data http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant sequence A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. http://purl.obolibrary.org/obo/SO_0000104 polypeptide http://purl.obolibrary.org/obo/SO_0000001 region polypeptide sequence A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity polymer A macromolecule is a 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. http://purl.obolibrary.org/obo/OBIws_0000001 digital document name http://purl.obolibrary.org/obo/IAO_0000300 textual entity file name A textual entity that refers to a digital document derived from a computer system. http://purl.obolibrary.org/obo/OBIws_0000019 gap separation distance setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification gap separation distance A software execution setting specification that specifies the distance between two consecutive gaps when aligning two sequences, within which introducing a new gap is penalized in addition to gap creation penalty. http://purl.obolibrary.org/obo/OBIws_0000020 end gap separation penalty setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification end gap separation penalty A software execution setting specification that states whether or not to apply the gap extension penalty when scoring terminal gaps using a Boolean value. configuration parameter which is a Boolean value, that states whether or not to apply the gap extension penalty when scoring terminal gaps. http://purl.obolibrary.org/obo/OBIws_0000021 number of iterations setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification number of iterations A software execution setting specification that specifies the maximum number of iterations to perform. http://purl.obolibrary.org/obo/OBIws_0000023 iteration strategy setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification iteration strategy A software execution setting specification that specifies the multiple alignment improvement iteration type. For clustalW, It can take values: none, tree(Iteration at each step of alignment process) or alignment(Iteration only on final alignment). http://purl.obolibrary.org/obo/OBIws_0000027 web service execution identifier http://purl.obolibrary.org/obo/IAO_0000577 CRID symbol job id A CRID symbol used to uniquely identify a submitted web service execution. http://purl.obolibrary.org/obo/OBIws_0000030 web service execution title http://purl.obolibrary.org/obo/IAO_0000300 textual entity job title A textual entity that is the name of a web service job submitted. http://purl.obolibrary.org/obo/OBIws_0000033 gap creation penalty setting specification http://purl.obolibrary.org/obo/OBIws_0000053 gap penalty setting specification gap creation penalty A gap penalty setting specification that specifies the penalty for introducing a new gap when producing an alignment. http://purl.obolibrary.org/obo/OBIws_0000038 gap extension penalty setting specification http://purl.obolibrary.org/obo/OBIws_0000053 gap penalty setting specification gap extension penalty A gap penalty setting specification that specifies the penalty for extending a gap when aligning sequences. http://purl.obolibrary.org/obo/OBIws_0000042 get web service execution status http://purl.obolibrary.org/obo/OBIws_0000104 web service execution get job status A web service execution that returns the status (e.g. Finished, Running) of a web service execution, depending upon web service execution identifier. . http://purl.obolibrary.org/obo/OBIws_0000044 get supported output data format http://purl.obolibrary.org/obo/OBIws_0000104 web service execution get result types A web service execution that retrieves all the supported output data format for a particular execution. http://purl.obolibrary.org/obo/OBIws_0000050 software execution http://purl.obolibrary.org/obo/OBI_0000011 planned process operation A planned process that realizes the concretization of a software. http://purl.obolibrary.org/obo/OBIws_0000053 gap penalty setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification gap penalty A software execution setting specification that specifies the penalty value for each gap introduced when aligning sequences (accounts for both gap creation and gap extension penalties). It has little affect on the speed or sensitivity except for extreme values. http://purl.obolibrary.org/obo/OBIws_0000056 number of match regions setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification number of matched regions A software execution setting specification that specifies the number of k-tuple matches on each diagonal used to create pairwise alignment. Decrease for speed; increase for sensitivity. http://purl.obolibrary.org/obo/OBIws_0000057 fast pairwise alignment scoring method setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification fast pairwise alignment scoring method A software execution setting specification that specifies the output type for fast pairwise alignment score (can be either percent or absolute). http://purl.obolibrary.org/obo/OBIws_0000060 alignment window size setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification alignment window size A software execution setting specification that specifies the number of diagonals around each of the 'best' diagonals that will be used for joining word matches. Decrease for speed; increase for sensitivity. http://purl.obolibrary.org/obo/OBIws_0000061 alignment word size setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification alignment word size A software execution setting specification that specifies the alignment word size used to find matches between the sequences. A higher value increases the speed of the alignment but decreases the sensitivity. http://purl.obolibrary.org/obo/OBIws_0000066 number of top combinations setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification number of top combinations A software execution setting specification that specifies the number of HSPs to be reported, such that any given HSP is allowed to be a member of just one set. Values: a numerical value or 'All' http://purl.obolibrary.org/obo/OBIws_0000067 pairwise alignment sensitivity setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification pairwise alignment sensitivity A software execution setting specification that specifies the sensitivity level of the search performed, it can take following values (very low, low,normal, medium, high). http://purl.obolibrary.org/obo/OBIws_0000068 pairwise alignment statistical model setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification pairwise alignment statistical model A software execution setting specification that specifies a statistical model to use for scoring alignments (pairwise). Can take values from (sum p, Poisson, kap). http://purl.obolibrary.org/obo/OBIws_0000072 inclusion of filtered sequences setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification inclusion of filtered sequences A software execution setting specification that specifies whether or not to show in the output file the query sequence used for the search, post filtering. Filtering here refers to masking of low complexity regions. http://purl.obolibrary.org/obo/OBIws_0000073 maximum match score setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification maximum match score A software execution setting specification that specifies the maximum number of match scores displayed in the output. http://purl.obolibrary.org/obo/OBIws_0000074 sequence range setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification sequence range A software execution setting specification that defines the range of query sequence to use for search. http://purl.obolibrary.org/obo/OBIws_0000075 maximum number of matched alignments setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification maximum number of matched alignment A software execution setting specification that specifies the maximum number of alignments displayed in the output. http://purl.obolibrary.org/obo/OBIws_0000077 drop-off score setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification drop-off score A software execution setting specification that determines the minimum allowable score for a sequence to be matched after which the algorithm gives up on aligning that sequence. http://purl.obolibrary.org/obo/OBIws_0000079 pairwise alignment hits ordering setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification pairwise alignment hits ordering A software execution setting specification that specifies the ordering criteria that is used to order the sequences (before displaying) that matched the search criteria. For example : The results could be ordered by the expectation value of sequences or using some other quantity like their score. http://purl.obolibrary.org/obo/OBIws_0000081 data format specification identifier http://purl.obolibrary.org/obo/IAO_0000028 symbol result type identifier WS annotations Group, UGA http://purl.obolibrary.org/obo/OBIws_0000082 sequence similarity expectation value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value expectation value A quantitative confidence value which determines a threshold value such that only alignments scoring more than this value are considered. http://purl.obolibrary.org/obo/OBIws_0000090 pairwise sequence alignment data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation pairwise sequence alignment A data transformation process that attempts to align two molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence. http://purl.obolibrary.org/obo/OBIws_0000091 local pairwise sequence alignment data transformation http://purl.obolibrary.org/obo/OBIws_0000090 pairwise sequence alignment data transformation local pairwise sequence alignment A pairwise sequence alignment data transformation that attempts to align two molecular sequences considering only parts of the sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence. http://purl.obolibrary.org/obo/OBIws_0000092 global multiple sequence alignment data transformation http://purl.obolibrary.org/obo/OBIws_0000117 multiple sequence alignment data transformation global multiple sequence alignment A multiple sequence alignment data transformation that attempts to align the sequences considering their entire length. http://purl.obolibrary.org/obo/OBIws_0000093 check web service execution status objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification check job status objective An objective specification that describes the goal of fetching the status of a web service execution. http://purl.obolibrary.org/obo/OBIws_0000094 record of missing annotation http://purl.obolibrary.org/obo/OBI_0000852 record of missing knowledge unannotated term A record of missing knowledge that describes terms in the document that are not present in the ontology. http://purl.obolibrary.org/obo/OBIws_0000095 match mismatch scores setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification match mismatch scores A software execution setting specification that specifies the scores for a match and miss-match, to be used when searching for similar nucleotide sequences. http://purl.obolibrary.org/obo/OBIws_0000096 BLAST analysis data transformation http://purl.obolibrary.org/obo/OBIws_0000091 local pairwise sequence alignment data transformation BLAST analysis A local pairwise sequence alignment data transformation that performs pairwise sequence alignment to search sequence databases for similar sequences. http://purl.obolibrary.org/obo/OBIws_0000099 gaps alignment setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification gaps alignment A software execution setting specification which specifies whether the gapped areas in query sequence should be aligned in the process of sequence alignment or not using a Boolean value. http://purl.obolibrary.org/obo/OBIws_0000104 web service execution http://purl.obolibrary.org/obo/OBIws_0000050 software execution web service operation A software execution that is provided by the web service, and involves invoking software execution over network. http://purl.obolibrary.org/obo/OBIws_0000106 sequence data format specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification sequence data format A data format specification for molecular sequence feature information. http://purl.obolibrary.org/obo/OBIws_0000107 fetch sequences objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification retrieve sequences objective An objective specification of retrieving a sequence from a sequence database given the sequence identifier and the database that has the sequence. http://purl.obolibrary.org/obo/OBIws_0000115 display histograms setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification display histograms A software execution setting specification that is used to specify whether histogram is returned with the result of FASTA search using true or false Boolean value. The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program. http://purl.obolibrary.org/obo/OBIws_0000116 slow pairwise sequence alignment data transformation http://purl.obolibrary.org/obo/OBIws_0000090 pairwise sequence alignment data transformation slow pairwise sequence alignment A pairwise sequence alignment data transformation that produces accurate alignments are carried out by using a dynamic programming method (Myers and Miller) to align every pair of sequences. http://purl.obolibrary.org/obo/OBIws_0000117 multiple sequence alignment data transformation http://purl.obolibrary.org/obo/OBI_0200000 data transformation multiple sequence alignment A data transformation that attempts to align multiple (more than two) molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence. http://purl.obolibrary.org/obo/OBIws_0000128 order of sequences in alignment setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification order of sequences in alignment A software execution setting specification that designates the order in which sequences appear in a final alignment. If ALIGNED option is chosen, the output order will be the order in which the sequences were aligned (from the guide tree/dendrogram). If INPUT option is chosen, the output will be in the same order as the input sequences. http://purl.obolibrary.org/obo/OBIws_0000133 web service execution status http://purl.obolibrary.org/obo/IAO_0000028 symbol job status A symbol that is used to specify the status of a web service execution. It usually takes one of following values - DONE, ERROR, NOT_FOUND,PENDING, RUNNING http://purl.obolibrary.org/obo/OBIws_0000139 fast pairwise sequence alignment data transformation http://purl.obolibrary.org/obo/OBIws_0000090 pairwise sequence alignment data transformation fast pairwise sequence alignment A pairwise sequence alignment data transformation that produces Fast/Approximate alignments using the method of Wilbur and Lipman (1983) and may be more suitable for sequences longer than 1000 residues. http://purl.obolibrary.org/obo/OBIws_0000149 display multiple HSPs setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification display multiple HSPs A software execution setting specification that specifies whether multiple high scoring alignments have to be displayed or not in the result using true or false Boolean value. http://purl.obolibrary.org/obo/OBIws_0000158 retrieve web service execution result http://purl.obolibrary.org/obo/OBIws_0000104 web service execution get result A web service execution that fetches the outcome of some previously executed web service operation (execution) given an execution identifier that is unique for that particular web service. http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification http://purl.obolibrary.org/obo/IAO_0000030 information content entity program setting parameter An information content entity which is an input setting parameter (usually optional) to some software execution that controls the way in which output is generated or displayed or which algorithm need to be executed. http://purl.obolibrary.org/obo/OBIws_0000169 comma separated values data format specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification CSV data format A data format specification that consists of any number of records and each record separated by a comma (','). http://purl.obolibrary.org/obo/OBIws_0000175 phylip execution identifier http://purl.obolibrary.org/obo/OBIws_0000027 web service execution identifier ITPPR A web service execution identifier that uniquely identifies a submitted a phylip web service execution. http://purl.obolibrary.org/obo/OBIws_0000184 transcript sequence data http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data Predicted RNA/mRNA Sequence (introns spliced out). A RNA sequence data that is about the primary structure of RNA sequence produced by transcription. http://purl.obolibrary.org/obo/OBIws_0000185 minimum signalp D score setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification min sigp D score A software execution setting specification that specifies the minimum value of D-score which is the average of the S-mean and Y-max score from SignalP-NN (neural network). http://purl.obolibrary.org/obo/OBIws_0000186 minimum signalp sum score setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification min sigp sum score A software execution setting specification that specifies the minimum value of signalP summary conclusion score. SignalP-NN (neural network) provides four scores and a conclusion for each such that the conclusion is 1 if the score meets a certain criteria and 0 otherwise. The SignalP summary conclusion is the sum of the four conclusions generated by SignalP, thus four is the highest score possible. We consider a summary conclusion score of three to be significant. http://purl.obolibrary.org/obo/OBIws_0000187 minimum signalp probability setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification min sigp signal probability A software execution setting specification that specifies the minimum value of signal probability from SignalP-HMM. http://purl.obolibrary.org/obo/OBIws_0000191 gene locus tag http://purl.obolibrary.org/obo/IAO_0000577 CRID symbol Gene ID A CRID symbol that is systematically applied to every gene in a genome within the context of sequencing projects. http://purl.obolibrary.org/obo/OBIws_0000193 coding sequence data http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data Coding Sequence A sequence data that is about primary structure of coding sequence of DNA. http://purl.obolibrary.org/obo/OBIws_0000194 protein sequence length http://purl.obolibrary.org/obo/IAO_0000027 data item Protein Length. A data item that represents length of predicted protein sequence. http://purl.obolibrary.org/obo/OBIws_0000196 genomic location of gene http://purl.obolibrary.org/obo/IAO_0000027 data item location text A data item indicates the location of a gene in the genome, which can influence the expression of the gene and functional interactions of the gene expression products. http://purl.obolibrary.org/obo/OBIws_0000198 maximum isoelectric point setting secification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification maximum isoelectric point A software execution setting specification that specifies the upper bound for the protein isoelectric point. http://purl.obolibrary.org/obo/OBIws_0000200 minimum isoelectric point setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification minimum isoelectric point A software execution setting specification that specifies the lower bound for the protein isoelectric point. http://purl.obolibrary.org/obo/OBIws_0000201 epitope confidence setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification epitope confidence A software execution setting specification that specifies the confidence of epitope present in predicted protein for a gene. This parameter can have combination High, Medium or Low as values. http://purl.obolibrary.org/obo/OBIws_0000202 find genes by transmembrane domain execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution find genes by transmembrane domain A web service execution that retrieves all genes having number of predicted transmembrane domains in a range that user specify. http://purl.obolibrary.org/obo/OBIws_0000203 find genes with epitopes execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution find genes with epitopes A web service execution that retrieves all genes whose encoding protein has an epitope identified by the Immune Epitope Database and Analysis Resource with the confidence specified by the user. http://purl.obolibrary.org/obo/OBIws_0000204 find genes by molecular weight execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution find genes by molecular weight A web service execution that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify. http://purl.obolibrary.org/obo/OBIws_0000205 minimum molecular weight setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification minimum molecular weight A software execution setting specification that specifies the minimum value for protein molecular weight. http://purl.obolibrary.org/obo/OBIws_0000206 maximum molecular weight setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification maximum molecular weight A software execution setting specification that specifies the maximum value for protein molecular weight. http://purl.obolibrary.org/obo/OBIws_0000207 maximum number of predicted transmembrane domains setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification maximum number of predicted transmembrane domains A software execution setting specification that specifies the upper bound on number of predicted transmembrane domains a protein may have. http://purl.obolibrary.org/obo/OBIws_0000208 find genes by isoelectric point execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution find genes by isoelectric point A web service execution that retrieves all genes whose protein product has an isoelectric point in a range that user specify. http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity http://purl.obolibrary.org/obo/BFO_0000040 material entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. http://purl.obolibrary.org/obo/BFO_0000005 dependent continuant http://purl.obolibrary.org/obo/BFO_0000002 continuant A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. 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_0000019 quality http://purl.obolibrary.org/obo/BFO_0000020 specifically dependent continuant A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property). 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_0000005 dependent continuant A 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_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/IAO_0000005 objective specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a 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://purl.obolibrary.org/obo/IAO_0000033 directive information entity a 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_0000010 software http://purl.obolibrary.org/obo/IAO_0000104 plan specification Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. http://purl.obolibrary.org/obo/IAO_0000028 symbol http://purl.obolibrary.org/obo/IAO_0000030 information content entity a smallish, word-like datum... http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/BFO_0000031 generically dependent continuant an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity http://purl.obolibrary.org/obo/IAO_0000033 directive information entity http://purl.obolibrary.org/obo/IAO_0000030 information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. http://purl.obolibrary.org/obo/IAO_0000064 algorithm http://purl.obolibrary.org/obo/IAO_0000104 plan specification A plan specification which describes inputs, 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_0000078 curation status specification http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. http://purl.obolibrary.org/obo/IAO_0000098 data format specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file http://purl.obolibrary.org/obo/IAO_0000100 data set http://purl.obolibrary.org/obo/IAO_0000027 data item A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. http://purl.obolibrary.org/obo/IAO_0000102 data about an ontology part http://purl.obolibrary.org/obo/IAO_0000027 data item data about an ontology part is a data item about a part of an ontology, for example a term http://purl.obolibrary.org/obo/IAO_0000104 plan specification http://purl.obolibrary.org/obo/IAO_0000033 directive information entity a 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/IAO_0000310 document http://purl.obolibrary.org/obo/IAO_0000030 information content entity A collection of information content entities intended to be understood together as a whole http://purl.obolibrary.org/obo/IAO_0000577 CRID symbol http://purl.obolibrary.org/obo/IAO_0000028 symbol A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry. http://purl.obolibrary.org/obo/OBI_0000011 planned process http://purl.obolibrary.org/obo/BFO_0000007 process A processual entity that realizes a plan which is the concretization of a plan specification. http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which is used to indicate the degree of uncertainty about a measurement. http://purl.obolibrary.org/obo/OBI_0000245 organization http://purl.obolibrary.org/obo/BFO_0000040 material entity An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. http://purl.obolibrary.org/obo/OBI_0000811 primary structure of DNA macromolecule http://purl.obolibrary.org/obo/SO_0000001 region a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. http://purl.obolibrary.org/obo/OBI_0000845 primary structure of RNA molecule http://purl.obolibrary.org/obo/SO_0000001 region The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together http://purl.obolibrary.org/obo/OBI_0000852 record of missing knowledge http://purl.obolibrary.org/obo/IAO_0000030 information content entity a information content entity created to indicate that information about something is not available to the person recording it. http://purl.obolibrary.org/obo/OBI_0000941 service consumer role http://purl.obolibrary.org/obo/BFO_0000023 role a role which inheres in a person who uses a service http://purl.obolibrary.org/obo/OBI_0000947 service provider role http://purl.obolibrary.org/obo/BFO_0000023 role is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person http://purl.obolibrary.org/obo/OBI_0000973 sequence data http://purl.obolibrary.org/obo/IAO_0000109 measurement datum A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. http://purl.obolibrary.org/obo/OBI_0001173 service http://purl.obolibrary.org/obo/OBI_0000011 planned process A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. http://purl.obolibrary.org/obo/OBI_0001573 DNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data item that is about the primary structure of DNA http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/BFO_0000040 material entity A material entity 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_0200081 sequence analysis objective http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. http://purl.obolibrary.org/obo/OBI_0200166 data transformation objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. http://purl.obolibrary.org/obo/CHEBI_16991 deoxyribonucleic acids http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid http://purl.obolibrary.org/obo/CHEBI_33839 macromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. http://purl.obolibrary.org/obo/CHEBI_33709 amino acids http://purl.obolibrary.org/obo/CHEBI_23367 molecular entity Carboxylic acids containing one or more amino groups. http://purl.obolibrary.org/obo/CHEBI_33697 ribonucleic acids http://purl.obolibrary.org/obo/CHEBI_33696 nucleic acid Naturally occurring polyribonucleotides. http://purl.obolibrary.org/obo/OBIws_0000003 file extension http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that is the suffix for a file name. http://purl.obolibrary.org/obo/OBIws_0000005 metadata of data format specification http://purl.obolibrary.org/obo/OBIws_0000001 digital document name A textual entity that gives the details of the different supported data formats and associated file extension and other metadata. http://purl.obolibrary.org/obo/OBIws_0000007 MIME type specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification A data format specification that is used to specify the content type over the Web. (MIME is an acronym for Multipurpose Internet Mail Extension) http://purl.obolibrary.org/obo/OBIws_0000013 clustering algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that assigns set of observations/data into subsets (called clusters) so that observations/data in the same cluster are similar in some sense. http://purl.obolibrary.org/obo/OBIws_0000014 sequence similarity identification objective http://purl.obolibrary.org/obo/OBI_0200081 sequence analysis objective A sequence analysis objective that describes the aim to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence. http://purl.obolibrary.org/obo/OBIws_0000015 pairwise sequence alignment algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences). http://purl.obolibrary.org/obo/OBIws_0000018 multiple sequence alignment algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that is used to obtain multiple sequence alignments between nucleotide or protein sequences. http://purl.obolibrary.org/obo/OBIws_0000024 algorithm identifier http://purl.obolibrary.org/obo/IAO_0000028 symbol A symbol that specifies a particular algorithm to be implemented in a tool or software. http://purl.obolibrary.org/obo/OBIws_0000025 multiple sequence alignment guide tree http://purl.obolibrary.org/obo/IAO_0000100 data set A data item which is a tree that represents the relationship between sequences and is used to build the multiple sequence alignment. For the first iteration of multiple sequence alignment process the guide tree is constructed by a clustering method while for the subsequent iterations it is constructed from the previous iteration. http://purl.obolibrary.org/obo/OBIws_0000026 retrieve alignment result objective http://purl.obolibrary.org/obo/OBIws_0000171 retrieve web service execution result objective A retrieve web service execution result objective that describes the goal of retrieving the sequence alignment result. http://purl.obolibrary.org/obo/OBIws_0000029 multiple sequence alignment data set http://purl.obolibrary.org/obo/OBIws_0000122 sequence alignment data set A sequence alignment data set that is produced as the output of a multiple sequence alignment process. http://purl.obolibrary.org/obo/OBIws_0000031 filter sequence data http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that filters sequence data depending on their similarity score to a specified sequence and expectation value. http://purl.obolibrary.org/obo/OBIws_0000034 DNA substitution matrix http://purl.obolibrary.org/obo/OBIws_0000051 scoring matrix A scoring matrix that is used for scoring alignment of nucleotide sequences. http://purl.obolibrary.org/obo/OBIws_0000036 protein distance matrix http://purl.obolibrary.org/obo/OBIws_0000100 matrix A Matrix that stores the evolutionary distance between each pair of protein sequences, with each species starting on a new line with the species name, followed by the distances to the species in order. http://purl.obolibrary.org/obo/OBIws_0000037 compute protein evolution distance execution http://purl.obolibrary.org/obo/OBIws_0000040 phylip execution A phylip execution that computes a protein evolution distance matrix using a amino acid replacement model. http://purl.obolibrary.org/obo/OBIws_0000039 construct phylip neighbor tree execution http://purl.obolibrary.org/obo/OBIws_0000040 phylip execution A phylip execution that constructs an unrooted phylogenetic tree from a protein distance matrix by successive clustering using either Neighbor joining or UPGMA method of clustering. http://purl.obolibrary.org/obo/OBIws_0000040 phylip execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that involves invocation of different programs for inferring phylogenetic relationships between groups of organisms. http://purl.obolibrary.org/obo/OBIws_0000043 clustalW execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that performs multiple sequence alignment. http://purl.obolibrary.org/obo/OBIws_0000045 retrieve alignment result execution http://purl.obolibrary.org/obo/OBIws_0000158 retrieve web service execution result A retrieve web service execution result that would fetch the result of alignment analysis given its unique execution identifier. http://purl.obolibrary.org/obo/OBIws_0000048 web service http://purl.obolibrary.org/obo/OBI_0001173 service A service that exposes an arbitrary set of operations which can be accessed through a programmatic interface to a web server maintained by the service provider. http://purl.obolibrary.org/obo/OBIws_0000049 amino acid substitution matrix http://purl.obolibrary.org/obo/OBIws_0000051 scoring matrix A scoring matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time. http://purl.obolibrary.org/obo/OBIws_0000051 scoring matrix http://purl.obolibrary.org/obo/OBIws_0000118 lower triangular matrix A lower triangular matrix where each cell represents a score to be assigned to a specific type of pairing of nucleotide or amino acid sequences generally used in sequence alignment. http://purl.obolibrary.org/obo/OBIws_0000055 invoke software execution over network objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification that a web service execution accomplishes. http://purl.obolibrary.org/obo/OBIws_0000063 multiple sequence alignment objective http://purl.obolibrary.org/obo/OBIws_0000014 sequence similarity identification objective A sequence similarity identification objective that aims to align multiple sequences at a time to determine the equivalence between them. http://purl.obolibrary.org/obo/OBIws_0000064 pairwise sequence alignment objective http://purl.obolibrary.org/obo/OBIws_0000014 sequence similarity identification objective A sequence similarity identification objective that aims to align two sequences at a time to determine the equivalence between them. http://purl.obolibrary.org/obo/OBIws_0000069 pairwise alignment data format specification http://purl.obolibrary.org/obo/OBIws_0000124 sequence alignment data format specification A data format specification that specifies the format for the data produced as a result of pairwise sequence alignment. e.g. BLASTXML http://purl.obolibrary.org/obo/OBIws_0000070 low complexity sequence filter algorithm identifier http://purl.obolibrary.org/obo/OBIws_0000071 sequence filter algorithm identifier A sequence filter algorithm identifier that specifies an algorithm to pre-process the query sequence, such that the low complexity regions in the sequence are filtered out before sequence alignment as low complexity regions tend to give a false estimate of the similarity score. http://purl.obolibrary.org/obo/OBIws_0000071 sequence filter algorithm identifier http://purl.obolibrary.org/obo/OBIws_0000024 algorithm identifier A data item which specifies a sequence filter that pre-processes the query sequence before alignment to remove the undesired portions of it. http://purl.obolibrary.org/obo/OBIws_0000076 gene strand specifier http://purl.obolibrary.org/obo/IAO_0000300 textual entity A textual entity that specifies the DNA strand, upper, lower or both of a specific gene to be considered in alignment. http://purl.obolibrary.org/obo/OBIws_0000078 sequence database for similarity search http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is stored on a computer and used for molecular sequence similarity search. http://purl.obolibrary.org/obo/OBIws_0000080 protein sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data that is about sequence of amino acids which are linked by peptide bonds. http://purl.obolibrary.org/obo/OBIws_0000083 retrieve signal peptide result http://purl.obolibrary.org/obo/OBIws_0000158 retrieve web service execution result A retrieve web service execution result that retrieves the outcome of a signal peptide prediction process given a unique web service execution identifier. http://purl.obolibrary.org/obo/OBIws_0000084 BLAST execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that performs local pairwise sequence alignment to search a database for similar sequences. http://purl.obolibrary.org/obo/OBIws_0000085 signal peptide prediction algorithm http://purl.obolibrary.org/obo/OBIws_0000154 protein signature recognition algorithm A protein signature prediction method that serves as a prediction model to predict the location of signal peptides in a protein sequence. http://purl.obolibrary.org/obo/OBIws_0000086 predicted protein signatures data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is as an outcome of protein signature prediction process. http://purl.obolibrary.org/obo/OBIws_0000088 BLAST algorithm http://purl.obolibrary.org/obo/OBIws_0000015 pairwise sequence alignment algorithm BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold. http://purl.obolibrary.org/obo/OBIws_0000097 sequence identifier http://purl.obolibrary.org/obo/IAO_0000577 CRID symbol A CRID symbol that serves as an identifier for a molecular sequence or for an entry from a molecular sequence database. http://purl.obolibrary.org/obo/OBIws_0000100 matrix http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is made up of a rectangular array of elements (or entries) set out by rows and columns. http://purl.obolibrary.org/obo/OBIws_0000101 fetch sequences execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that retrieves the sequence given the sequence identifier and the sequence database that has the sequence. http://purl.obolibrary.org/obo/OBIws_0000102 predict signal peptides http://purl.obolibrary.org/obo/OBIws_0000163 identify protein signature execution An identify protein signature execution that attempts to predict the presence and location of signal peptide cleavage sites in a protein sequence. http://purl.obolibrary.org/obo/OBIws_0000103 predict signal peptide cleavage sites objective http://purl.obolibrary.org/obo/OBIws_0000170 identify protein signature objective An identify protein signature objective that describes the goal of predicting the presence and location of signal peptide cleavage sites in an amino acid sequence. http://purl.obolibrary.org/obo/OBIws_0000118 lower triangular matrix http://purl.obolibrary.org/obo/OBIws_0000100 matrix A matrix with equal number of rows and columns for which all the elements above the main diagonal have values equal to 0. http://purl.obolibrary.org/obo/OBIws_0000122 sequence alignment data set http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is produced as the output of some sequence alignment process. http://purl.obolibrary.org/obo/OBIws_0000124 sequence alignment data format specification http://purl.obolibrary.org/obo/IAO_0000098 data format specification A data format specification that specifies the data format for the outcome of sequence alignment (pairwise or multiple) process. http://purl.obolibrary.org/obo/OBIws_0000126 multiple sequence alignment data format specification http://purl.obolibrary.org/obo/OBIws_0000124 sequence alignment data format specification A data format specification that specifies the format for the data produced as a result of multiple sequence alignment. e.g. FASTA, PHYLIP, ALN W/Numbers http://purl.obolibrary.org/obo/OBIws_0000147 filter sequence data objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification that describes the goal of filtering sequence data depending on their similarity score to a specified sequence and expectation value. http://purl.obolibrary.org/obo/OBIws_0000148 retrieve signal peptide result objective http://purl.obolibrary.org/obo/OBIws_0000171 retrieve web service execution result objective A retrieve web service execution result objective that describes the goal of retrieving the result of an operation to predict the presence and location of signal peptide cleavage sites in amino acid sequences. http://purl.obolibrary.org/obo/OBIws_0000150 retrieve supported output data format objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification that describes the goal of retrieving the supported output data formats for a particular web service execution. http://purl.obolibrary.org/obo/OBIws_0000152 base64 encoding specification http://purl.obolibrary.org/obo/OBIws_0000007 MIME type specification A MIME type specification which represents an encoding scheme that represent binary data in an ASCII string format by translating it into a radix-64 representation. http://purl.obolibrary.org/obo/OBIws_0000154 protein signature recognition algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm or a predictive model to predict the presence of a particular protein signature. http://purl.obolibrary.org/obo/OBIws_0000159 signal peptide prediction score http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which is a score assigned for a signal peptide region predicted by a signal peptide prediction algorithm. http://purl.obolibrary.org/obo/OBIws_0000161 signal peptide prediction threshold value http://purl.obolibrary.org/obo/OBI_0000071 quantitative confidence value A quantitative confidence value that acts as a threshold score to determine if the sequence pattern in consideration is a signal peptide or not. http://purl.obolibrary.org/obo/OBIws_0000163 identify protein signature execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that tries to locate occurrence of different known protein signatures like signal peptides in a protein sequence. http://purl.obolibrary.org/obo/OBIws_0000167 signal peptides prediction outcome http://purl.obolibrary.org/obo/IAO_0000027 data item A data item which is the outcome of predict signal peptide cleavage sites execution that specifies if a signal peptide chain is found or not. http://purl.obolibrary.org/obo/OBIws_0000170 identify protein signature objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification that describes the goal of identifying protein signatures in a protein sequence. http://purl.obolibrary.org/obo/OBIws_0000171 retrieve web service execution result objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification that describes the goal of retrieving the outcome of some previously executed web service execution. http://purl.obolibrary.org/obo/OBIws_0000172 predicted signal peptide cleavage sites data set http://purl.obolibrary.org/obo/OBIws_0000086 predicted protein signatures data set A predicted signal peptide cleavage sites data set that includes the outcome and all the meta data of signal peptide cleavage sites prediction process. http://purl.obolibrary.org/obo/OBIws_0000176 construct phylogenetic trees objective http://purl.obolibrary.org/obo/OBI_0200081 sequence analysis objective A sequence analysis objective that describes the goal of constructing a phylogenetic tree that shows inferred evolutionary relationships between protein sequences. http://purl.obolibrary.org/obo/OBIws_0000177 consensus tree construction algorithm http://purl.obolibrary.org/obo/IAO_0000064 algorithm An algorithm that is the method for construction of consensus tree. http://purl.obolibrary.org/obo/OBIws_0000178 phylogenetic tree http://purl.obolibrary.org/obo/IAO_0000100 data set A data set which is a tree that represents evolutionary relationships between species, where the length of branches of the tree can signify evolutionary distance. http://purl.obolibrary.org/obo/OBIws_0000179 evolution based amino acid substitution matrix http://purl.obolibrary.org/obo/OBIws_0000049 amino acid substitution matrix An amino acid substitution matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time calculated using an empirical model for protein evolution. http://purl.obolibrary.org/obo/OBIws_0000180 compute protein evolution distance objective http://purl.obolibrary.org/obo/OBI_0200081 sequence analysis objective A sequence analysis objective that aims to compute a protein distance matrix for a multiple sequence alignment using a suitable amino acid replacement model. http://purl.obolibrary.org/obo/OBIws_0000181 consensus tree http://purl.obolibrary.org/obo/OBIws_0000178 phylogenetic tree A phylogenetic tree that is a cladogram which summarizes agreement between two or more phylogenetic trees. http://purl.obolibrary.org/obo/OBIws_0000182 genetic code http://purl.obolibrary.org/obo/IAO_0000100 data set A data set that is a set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences). http://purl.obolibrary.org/obo/OBIws_0000183 construct consensus tree execution http://purl.obolibrary.org/obo/OBIws_0000040 phylip execution A phylip execution that constructs a consensus tree that summarizes the agreement between two or more phylogenetic trees. http://purl.obolibrary.org/obo/OBIws_0000188 any or all signalp setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification A software execution setting specification that specifies Union or intersection of advanced parameters. http://purl.obolibrary.org/obo/OBIws_0000189 find genes objective http://purl.obolibrary.org/obo/IAO_0000005 objective specification An objective specification of retrieving genes based on different parameters (e.g., gene locus tag, taxonomy or signal peptide etc.). http://purl.obolibrary.org/obo/OBIws_0000190 find genes by taxonomy execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that retrieves all genes of one or more species/organism(s). http://purl.obolibrary.org/obo/OBIws_0000192 RNA sequence data http://purl.obolibrary.org/obo/OBI_0000973 sequence data A sequence data that is about the primary structure of RNA. http://purl.obolibrary.org/obo/OBIws_0000195 find genes using signal peptide execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that retrieves all genes that are predicted to encode a signal peptide. http://purl.obolibrary.org/obo/OBIws_0000197 find genes by locus tag execution http://purl.obolibrary.org/obo/OBIws_0000104 web service execution A web service execution that retrieves genes using list of comma separated gene locus tag. http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute http://purl.obolibrary.org/obo/BFO_0000019 quality An attribute to describe the kind of biological sequence. http://purl.obolibrary.org/obo/BFO_0000007 process http://purl.obolibrary.org/obo/BFO_0000003 occurrent A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. http://purl.obolibrary.org/obo/NCBITaxon_9606 Homo sapiens http://purl.obolibrary.org/obo/NCBITaxon_9605 Homo human being http://purl.obolibrary.org/obo/OBIws_0000199 minimum number of predicted transmembrane domains setting specification http://purl.obolibrary.org/obo/OBIws_0000165 software execution setting specification minimum number of predicted transmembrane domains http://purl.obolibrary.org/obo/NCBITaxon_33511 Deuterostomia http://purl.obolibrary.org/obo/NCBITaxon_33316 Coelomata http://purl.obolibrary.org/obo/IAO_0000429 email address http://purl.obolibrary.org/obo/IAO_0000030 information content entity http://purl.obolibrary.org/obo/NCBITaxon_10239 Viruses http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2157 Archaea http://purl.obolibrary.org/obo/OBI_0100026 organism http://purl.obolibrary.org/obo/NCBITaxon_2 Bacteria 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/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_117570 Teleostomi http://purl.obolibrary.org/obo/NCBITaxon_8287 Sarcopterygii http://purl.obolibrary.org/obo/NCBITaxon_117571 Euteleostomi http://purl.obolibrary.org/obo/NCBITaxon_33154 Fungi/Metazoa group http://purl.obolibrary.org/obo/NCBITaxon_2759 Eukaryota http://purl.obolibrary.org/obo/NCBITaxon_9443 Primates http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_32524 Amniota http://purl.obolibrary.org/obo/NCBITaxon_9347 Eutheria http://purl.obolibrary.org/obo/NCBITaxon_32525 Theria http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_33154 Fungi/Metazoa group http://purl.obolibrary.org/obo/NCBITaxon_6072 Eumetazoa http://purl.obolibrary.org/obo/NCBITaxon_33208 Metazoa http://purl.obolibrary.org/obo/NCBITaxon_33316 Coelomata http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_7711 Chordata http://purl.obolibrary.org/obo/NCBITaxon_33511 Deuterostomia http://purl.obolibrary.org/obo/NCBITaxon_32525 Theria http://purl.obolibrary.org/obo/NCBITaxon_40674 Mammalia http://purl.obolibrary.org/obo/NCBITaxon_33213 Bilateria http://purl.obolibrary.org/obo/NCBITaxon_6072 Eumetazoa http://purl.obolibrary.org/obo/NCBITaxon_89593 Craniata http://purl.obolibrary.org/obo/NCBITaxon_7711 Chordata http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_117570 Teleostomi http://purl.obolibrary.org/obo/NCBITaxon_7776 Gnathostomata http://purl.obolibrary.org/obo/NCBITaxon_32523 Tetrapoda http://purl.obolibrary.org/obo/NCBITaxon_8287 Sarcopterygii http://purl.obolibrary.org/obo/NCBITaxon_7742 Vertebrata http://purl.obolibrary.org/obo/NCBITaxon_89593 Craniata http://purl.obolibrary.org/obo/NCBITaxon_314146 Euarchontoglires http://purl.obolibrary.org/obo/NCBITaxon_9347 Eutheria http://purl.obolibrary.org/obo/NCBITaxon_9605 Homo http://purl.obolibrary.org/obo/NCBITaxon_207598 Homo/Pan/Gorilla group http://purl.obolibrary.org/obo/NCBITaxon_9526 Catarrhini http://purl.obolibrary.org/obo/NCBITaxon_314293 Simiiformes http://purl.obolibrary.org/obo/NCBITaxon_9604 Hominidae http://purl.obolibrary.org/obo/NCBITaxon_314295 Hominoidea http://purl.obolibrary.org/obo/NCBITaxon_314293 Simiiformes http://purl.obolibrary.org/obo/NCBITaxon_376913 Haplorrhini http://purl.obolibrary.org/obo/NCBITaxon_376913 Haplorrhini http://purl.obolibrary.org/obo/NCBITaxon_9443 Primates http://purl.obolibrary.org/obo/NCBITaxon_314295 Hominoidea http://purl.obolibrary.org/obo/NCBITaxon_9526 Catarrhini http://purl.obolibrary.org/obo/NCBITaxon_207598 Homo/Pan/Gorilla group http://purl.obolibrary.org/obo/NCBITaxon_9604 Hominidae http://purl.obolibrary.org/obo/BFO_0000001 entity http://purl.obolibrary.org/obo/IAO_0000219 denotes http://purl.obolibrary.org/obo/IAO_0000136 is about denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically http://purl.obolibrary.org/obo/OBI_0000293 has_specified_input http://purl.obolibrary.org/obo/BFO_0000057 has participant A relation between a planned process and a continuant participating in that process that is not created during the process. 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_0000295 is_specified_input_of http://purl.obolibrary.org/obo/BFO_0000056 participates in A relation between a planned process and a continuant participating in that process that is not created during the process. 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_0000299 has_specified_output http://purl.obolibrary.org/obo/BFO_0000057 has participant A relation between a planned process and a continuant participating in that process. The presence of 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_0000312 is_specified_output_of http://purl.obolibrary.org/obo/BFO_0000056 participates in A relation between a planned process and a continuant participating in that process. The presence of 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/BFO_0000052 inheres in http://purl.obolibrary.org/obo/BFO_0000070 s depends on inheres_in http://purl.obolibrary.org/obo/BFO_0000050 is part of http://purl.obolibrary.org/obo/BFO_0000082 is located in part_of http://purl.obolibrary.org/obo/IAO_0000136 is about is_about is a (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/OBI_0000417 achieves_planned_objective This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. http://purl.obolibrary.org/obo/BFO_0000056 participates in participates_in http://purl.obolibrary.org/obo/BFO_0000057 has participant has_participant http://purl.obolibrary.org/obo/BFO_0000054 is realized by realized_by http://purl.obolibrary.org/obo/BFO_0000051 has part has_part http://purl.obolibrary.org/obo/BFO_0000053 is bearer of bearer_of http://purl.obolibrary.org/obo/BFO_0000070 s depends on s_depends_on http://purl.obolibrary.org/obo/BFO_0000082 is located in located_in http://purl.obolibrary.org/obo/BFO_0000058 is concretization of concretization_of http://purl.obolibrary.org/obo/BFO_0000055 realizes http://purl.obolibrary.org/obo/OBIws_0000054 has_dimension http://purl.obolibrary.org/obo/OBIws_0000062 has_description http://purl.obolibrary.org/obo/OBIws_0000130 is_encoded_in http://purl.obolibrary.org/obo/OBIws_0000132 is_encoded_of http://purl.obolibrary.org/obo/OBIws_0000136 has_value http://purl.obolibrary.org/obo/OBIws_0000137 is_executed_in http://purl.obolibrary.org/obo/OBIws_0000138 is_executed_of http://purl.obolibrary.org/obo/BFO_0000059 concretizes