Release v1.1 This file is based on checkout of our SVN repository revision $Revision: 61 $ 2012-12-18 en Akshay Choche Alok Dhamanaskar An ontology for the annotation of bioinformatics web services. An ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services. Chaitanya Guttula Chris Stoeckert Jessie Kissinger Jie Zheng John Miller Description An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. has_specified_input 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input 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. PERSON: Alan Ruttenberg see is_input_of example_of_usage definition GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg curator note term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober term editor has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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. PERSON: Alan Ruttenberg alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example is part of There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else part of part_of has part has_part inheres in inheres_in is bearer of bearer of bearer_of is realized by realized by realized_by realizes participates in participates_in has participant has_participant is concretization of concretization of concretization_of concretizes s depends on s_depends_on is located in located in located_in is about 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. Smith, Ceusters, Ruttenberg, 2000 years of philosophy This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg denotes 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan 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 person:Alan Ruttenberg has_specified_input 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input 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. PERSON: Alan Ruttenberg see is_input_of example_of_usage is_specified_input_of PERSON:Bjoern Peters is_specified_input_of 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. Alan Ruttenberg some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output 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. PERSON: Alan Ruttenberg is_specified_output_of PERSON:Bjoern Peters is_specified_output_of 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. Alan Ruttenberg achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived 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. achieves_planned_objective modified according to email thread from 1/23/09 in accordince with DT and PPPB branch is_encoded_in SWO proposed relation, link data with data format specification, or software with program language is_encoded_of is_executed_in propose to deprecate algorithm/software is_executed_in information process is_executed_of propose to deprecate has_dimension has_description has_value entity entity continuant 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. a heart a person a symphony orchestra continuant endurant the color of a tomato the disposition of blood to coagulate the lawn and atmosphere in front of our building the mass of a cloud occurrent An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. a surgical operation as processual context for a nosocomical infection occurrent perdurant the life of an organism the most interesting part of Van Gogh's life the spatiotemporal context occupied by a process of cellular meiosis the spatiotemporal region occupied by the development of a cancer tumor independent 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. a chair a heart a leg a person a symphony orchestra an organism independent continuant substantial entity the bottom right portion of a human torso the lawn and atmosphere in front of our building dependent continuant A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities. dependent continuant process A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. process the life of an organism the process of cell-division the process of sleeping realizable entity 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. If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. realizable entity the disposition of blood to coagulate the disposition of metal to conduct electricity the function of the reproductive organs the role of being a doctor quality A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property). quality the ambient temperature of air the circumference of a waist the color of a tomato the mass of a piece of gold the shape of a nose the weight of a chimpanzee specifically dependent continuant 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. mode property specifically dependent continuant the color of a tomato the disposition of fish to decay the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. the liquidity of blood the mass of a cloud the role of being a doctor the smell of mozzarella trope role 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. role the role of a biological grandfather as legal guardian in the context of a system of laws the role of a chemical compound in an experiment the role of a patient relative as defined by a hospital administrative form the role of a person as a surgeon the role of a student in a university the role of a woman as a legal mother in the context of system of laws the role of ingested matter in digestion generically 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. a certain PDF file that exists in different and in several hard drives generically dependent continuant material entity An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Examples: collection of random bacteria, a chair, dorsal surface of the body Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. material entity deoxyribonucleic acids High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. deoxyribonucleic acids molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity nucleic acid 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. nucleic acid ribonucleic acids Naturally occurring polyribonucleotides. ribonucleic acids amino acids Carboxylic acids containing one or more amino groups. amino acids macromolecule 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. macromolecule polymer objective specification 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." Answers the question, why did you do this experiment? OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel 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. objective specification purpose of a study; support of hypothesis, discovery of new information action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take datum label 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. 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 GROUP: IAO datum label http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 software data item 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. Data items include counts of things, analyte concentrations, and statistical summaries. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees 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. data data item symbol 20091104, MC: this needs work and will most probably change PERSON: Jonathan Rees a smallish, word-like datum... symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information content entity information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. directive information entity 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan algorithm 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. OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug 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. curation status specification data format specification 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" 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 OBI branch derived OBI_0000187 PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch data format specification data set 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 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. Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). OBI_0000042 data set group:OBI person:Allyson Lister person:Chris Stoeckert data about an ontology part Person:Alan Ruttenberg data about an ontology part is a data item about a part of an ontology, for example a term plan specification 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. 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. plan specification measurement datum 2/2/2009 is_specified_output of some assay? A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. OBI_0000305 group:OBI measurement datum person:Chris Stoeckert textual entity 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. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities text textual entity document A collection of information content entities intended to be understood together as a whole A journal article, patent application, laboratory notebook, or a book PERSON: Lawrence Hunter document email address Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583 Person:Alan Ruttenberg Person:Chris Stoeckart email address CRID symbol A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry. IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded. Original proposal from Bjoern, discussions at IAO calls PERSON: Alan Ruttenberg PERSON: Bill Hogan PERSON: Bjoern Peters PERSON: Melanie Courtot PMID:12345, 12345 in a database column which has header "pubmedID" Viruses Viruses Teleostomi Teleostomi Euteleostomi Euteleostomi Bacteria Bacteria Homo/Pan/Gorilla group Homo/Pan/Gorilla group Archaea Archaea Eukaryota Eukaryota Euarchontoglires Euarchontoglires Simiiformes Simiiformes Hominoidea Hominoidea Tetrapoda Tetrapoda Amniota Amniota Theria Theria Fungi/Metazoa group Fungi/Metazoa group Metazoa Metazoa Bilateria Bilateria Coelomata Coelomata Deuterostomia Deuterostomia Haplorrhini Haplorrhini Mammalia Mammalia Eumetazoa Eumetazoa Chordata Chordata Vertebrata Vertebrata Gnathostomata Gnathostomata Sarcopterygii Sarcopterygii Craniata Craniata Eutheria Eutheria Primates Primates Catarrhini Catarrhini Hominidae Hominidae Homo Homo Homo sapiens human being Homo sapiens planned process 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) 6/11/9: Edited at workshop. Used to include: is initiated by an agent Bjoern Peters Injecting mice with a vaccine in order to test its efficacy We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. branch derived A processual entity that realizes a plan which is the concretization of a plan specification. This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process quantitative confidence value group:OBI A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert quantitative confidence value organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone 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. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. organization primary structure of DNA macromolecule BP et al a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues. placeholder for SO primary structure of DNA macromolecule primary structure of RNA molecule Person:Bjoern Peters 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 primary structure of RNA molecule record of missing knowledge A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured. Bjoern Peters This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately. a information content entity created to indicate that information about something is not available to the person recording it. record of missing knowledge service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer OBI Person:Helen Parkinson a role which inheres in a person who uses a service service consumer role service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. PERSON:Helen Parkinson 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 service provider role sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. GROUP: OBI Person:Chris Stoeckert example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. sequence data service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony service DNA sequence data 8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. A sequence data item that is about the primary structure of DNA DNA sequence data OBI call; Bjoern Peters OBI call; Melanie Courtout The part of a FASTA file that contains the letters ACTGGGAA organism 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch 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. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus data transformation Philippe Rocca-Serra The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value. A data transformation is a process which produces output data from input data Branch editors Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing data transformation sequence analysis objective James Malone PERSON: James Malone A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. sequence analysis objective data transformation objective A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. James Malone PERSON: James Malone data transformation objective normalize objective digital document name ITPPR A textual entity that refers to a digital document derived from a computer system. ITPPR file name file extension A textual entity that is the suffix for a file name. EDAM: file extension WS annotations Group, UGA metadata of data format specification A textual entity that gives the details of the different supported data formats and associated file extension and other metadata. WS annotations Group, UGA ClustalW Web service Documentation MIME type 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) Ready for OBI-WS : v1.0 Wikipedia: en.wikipedia.org/wiki/MIME WS Annotations Group, UGA clustering algorithm WS Annotations Group, UGA Ready for OBI-WS : v1.0 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. Wikipedia: en.wikipedia.org/wiki/Nearest_neighbor_search sequence similarity identification objective A sequence analysis objective that describes the aim to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence. ITPPR EDAM: alignment Ready for OBI-WS : v1.0 pairwise sequence alignment algorithm An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences). WS Annotations Group, UGA WS Annotations Group, UGA Ready for OBI-WS : v1.0 multiple sequence alignment algorithm An algorithm that is used to obtain multiple sequence alignments between nucleotide or protein sequences. Ready for OBI-WS : v1.0 ITPPR ITPPR gap separation distance setting specification ClustalW Web service Documentation and WS annotations Group, UGA 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. WS Annotations Group, UGA gap separation distance end gap separation penalty setting specification End Gap Separation: Treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above). If you turn this off, end gaps will be ignored for this purpose. This is useful when you wish to align fragments where the end gaps are not biologically meaningful. WS Annotations Group, UGA end gap separation penalty ClustalW Web service Documentation and WS annotations Group, UGA 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. number of iterations setting specification number of iterations ClustalW Web service Documentation WS Annotations Group, UGA A software execution setting specification that specifies the maximum number of iterations to perform. iteration strategy setting specification ClustalW Web service Documentation iteration strategy WS Annotations Group, UGA 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). algorithm identifier ITPPR ITPPR A symbol that specifies a particular algorithm to be implemented in a tool or software. multiple sequence alignment guide tree 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. Wikipedia : http://en.wikipedia.org/wiki/Multiple_sequence_alignment ITPPR retrieve alignment result objective ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa A retrieve web service execution result objective that describes the goal of retrieving the sequence alignment result. Ready for OBI-WS : v1.0 WS Annotations Group, UGA web service execution identifier Unique identifier for Web Service job job id A CRID symbol used to uniquely identify a submitted web service execution. ITPPR ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa multiple sequence alignment data set WS Annotations Group, UGA A sequence alignment data set that is produced as the output of a multiple sequence alignment process. WS Annotations Group, UGA web service execution title job title ClustalW Web service Documentation A textual entity that is the name of a web service job submitted. ITPPR filter sequence data A web service execution that filters sequence data depending on their similarity score to a specified sequence and expectation value. ITPPR ITPPR gap creation penalty setting specification A gap penalty setting specification that specifies the penalty for introducing a new gap when producing an alignment. gap creation penalty EDAM: gap creation penalty WS Annotations Group, UGA DNA substitution matrix A scoring matrix that is used for scoring alignment of nucleotide sequences. WS annotations Group, UGA WS annotations Group, UGA protein distance 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. WS annotations Group, UGA http://cmgm.stanford.edu/phylip/protdist.html compute protein evolution distance execution A phylip execution that computes a protein evolution distance matrix using a amino acid replacement model. ITPPR http://cmgm.stanford.edu/phylip/protdist.html#0 gap extension penalty setting specification Ready for OBI-WS : v1.0 gap extension penalty WS Annotations Group, UGA EDAM: gap extension penalty A gap penalty setting specification that specifies the penalty for extending a gap when aligning sequences. construct phylip neighbor tree 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. ITPPR http://evolution.genetics.washington.edu/phylip/doc/neighbor.html phylip execution A web service execution that involves invocation of different programs for inferring phylogenetic relationships between groups of organisms. http://en.wikipedia.org/wiki/Phylogenetics, http://www.phylip.com/ ITPPR get web service execution status ITPPR A web service execution that returns the status (e.g. Finished, Running) of a web service execution, depending upon web service execution identifier. . ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa get job status clustalW execution ClustalW Web service Documentation A web service execution that performs multiple sequence alignment. ITPPR get supported output data format A web service execution that retrieves all the supported output data format for a particular execution. ITPPR ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa get result types retrieve alignment result execution ClustalW Web service Documentation WS annotations Group, UGA A retrieve web service execution result that would fetch the result of alignment analysis given its unique execution identifier. web 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. Wikipedia: http://en.wikipedia.org/wiki/Web_service ITPPR amino acid substitution matrix There are two options for the protein weight matrix: BLOSUM and PAM. The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance. WS annotations Group, UGA http://en.wikipedia.org/wiki/Substitution_matrix A scoring matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time. software execution ITPPR ITPPR operation A planned process that realizes the concretization of a software. scoring 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. WS annotations Group, UGA WS annotations Group, UGA gap penalty setting specification WS Annotations Group, UGA EDAM: gap Penalty 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. invoke software execution over network objective ITPPR ITPPR An objective specification that a web service execution accomplishes. Ready for OBI-WS : v1.0 number of match regions 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. ClustalW Web service Documentation WS Annotations Group, UGA fast pairwise alignment scoring method setting specification ClustalW Web service Documentation A software execution setting specification that specifies the output type for fast pairwise alignment score (can be either percent or absolute). WS Annotations Group, UGA fast pairwise alignment scoring method alignment window size setting specification WS Annotations Group, UGA alignment window size ClustalW Web service Documentation 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. alignment word size setting specification ClustalW Web service Documentation WS Annotations Group, UGA 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. multiple sequence alignment objective A sequence similarity identification objective that aims to align multiple sequences at a time to determine the equivalence between them. Ready for OBI-WS : v1.0 ITPPR EDAM: alignment & ITPPR pairwise sequence alignment objective A sequence similarity identification objective that aims to align two sequences at a time to determine the equivalence between them. WS Annotations Group, UGA WS Annotations Group, UGA Ready for OBI-WS : v1.0 number of top combinations setting specification 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' ITPPR WU-Blast Web service documentation number of top combinations pairwise alignment sensitivity setting specification 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). ITPPR WU-Blast Web service documentation pairwise alignment sensitivity pairwise alignment statistical model setting specification A software execution setting specification that specifies a statistical model to use for scoring alignments (pairwise). Can take values from (sum p, Poisson, kap). WU-BLAST Web service documentation ITPPR pairwise alignment statistical model pairwise 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 Ready for OBI-WS : v1.0 WUBlast Web service documentation ITPPR low complexity 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://www.ebi.ac.uk/Tools/sss/wublast/help/index-protein.html#filter ITPPR sequence filter 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. WU-BLAST Web service documentation ITPPR inclusion of filtered sequences setting specification 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. WU-BLAST Web service documentation inclusion of filtered sequences ITPPR maximum match score setting specification A software execution setting specification that specifies the maximum number of match scores displayed in the output. ITPPR maximum match score WU-BLAST Web service documentation sequence range setting specification A software execution setting specification that defines the range of query sequence to use for search. ITPPR sequence range NCBI BLAST Web service documentation maximum number of matched alignments setting specification A software execution setting specification that specifies the maximum number of alignments displayed in the output. WU-BLAST Web service documentation maximum number of matched alignment ITPPR gene strand specifier A textual entity that specifies the DNA strand, upper, lower or both of a specific gene to be considered in alignment. ITPPR WU-BLAST Web service documentation drop-off score setting specification 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. ITPPR drop-off score NCBI BLAST Web service documentation sequence database for similarity search A data set that is stored on a computer and used for molecular sequence similarity search. WEBSITE:http://en.wikipedia.org/wiki/Sequence_database ITPPR pairwise alignment hits ordering setting specification 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. WU-BLAST Web service documentation pairwise alignment hits ordering ITPPR protein sequence data OBI / ITPPR A sequence data that is about sequence of amino acids which are linked by peptide bonds. ITPPR data format specification identifier A symbol used to identify (uniquely for a particular web service) the output type. result type identifier WS annotations Group, UGA WS annotations Group, UGA sequence similarity expectation value A quantitative confidence value which determines a threshold value such that only alignments scoring more than this value are considered. expectation value WUBlast Web service documentation ITPPR retrieve signal peptide result ITPPR SignalP Web service documentation A retrieve web service execution result that retrieves the outcome of a signal peptide prediction process given a unique web service execution identifier. BLAST execution A web service execution that performs local pairwise sequence alignment to search a database for similar sequences. ITPPR ITPPR It is getting inferred as a Sequence alignment data Transformation is that what we want signal peptide prediction algorithm SignalP Web service documentation A protein signature prediction method that serves as a prediction model to predict the location of signal peptides in a protein sequence. ITPPR predicted protein signatures data set ITPPR InterProScan Documentation A data set that is as an outcome of protein signature prediction process. BLAST 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. Wikipedia: BLAST Ready for OBI-WS : v1.0 ITPPR pairwise sequence alignment data transformation 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. Ready for OBI-WS : v1.0 EDAM: alignment & WS Annotations Group, UGA ITPPR pairwise sequence alignment local pairwise sequence alignment data transformation 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. local pairwise sequence alignment ITPPR Ready for OBI-WS : v1.0 EDAM: alignment & WS Annotations Group, UGA global multiple sequence alignment data transformation A multiple sequence alignment data transformation that attempts to align the sequences considering their entire length. WS Annotations Group, UGA global multiple sequence alignment Ready for OBI-WS : v1.0 ITPPR check web service execution status objective An objective specification that describes the goal of fetching the status of a web service execution. Ready for OBI-WS : v1.0 ITPPR check job status objective record of missing annotation A record of missing knowledge that describes terms in the document that are not present in the ontology. unannotated term WS Annotations Group, UGA ITPPR match mismatch scores setting specification A software execution setting specification that specifies the scores for a match and miss-match, to be used when searching for similar nucleotide sequences. NCBI BLAST Web service documentation ITPPR match mismatch scores BLAST analysis data transformation A local pairwise sequence alignment data transformation that performs pairwise sequence alignment to search sequence databases for similar sequences. BLAST analysis WS Annotations Group, UGA Documentation for BLAST at NCBI Ready for OBI-WS : v1.0 sequence identifier A CRID symbol that serves as an identifier for a molecular sequence or for an entry from a molecular sequence database. EDAM: sequence identifier ITPPR gaps alignment setting specification 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. ITPPR NCBIBlast Web service documentation gaps alignment matrix WS annotations Group, UGA Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29 A data set that is made up of a rectangular array of elements (or entries) set out by rows and columns. fetch sequences execution A web service execution that retrieves the sequence given the sequence identifier and the sequence database that has the sequence. ITPPR ITPPR predict signal peptides An identify protein signature execution that attempts to predict the presence and location of signal peptide cleavage sites in a protein sequence. SignalP Web service documentation ITPPR predict signal peptide cleavage sites 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. ITPPR Ready for OBI-WS : v1.0 SignalP Web service documentation web service execution A software execution that is provided by the web service, and involves invoking software execution over network. ITPPR ITPPR web service operation sequence data format specification A data format specification for molecular sequence feature information. EDAM sequence data format ITPPR Ready for OBI-WS : v1.0 fetch sequences objective An objective specification of retrieving a sequence from a sequence database given the sequence identifier and the database that has the sequence. retrieve sequences objective ITPPR Ready for OBI-WS : v1.0 ITPPR display histograms setting specification 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. display histograms FASTA Web service documentation slow pairwise sequence alignment data transformation 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. Ready for OBI-WS : v1.0 ClustalW Documentation ITPPR slow pairwise sequence alignment multiple sequence alignment data transformation WS Annotations Group, UGA multiple sequence alignment Ready for OBI-WS : v1.0 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. ITPPR lower triangular matrix A matrix with equal number of rows and columns for which all the elements above the main diagonal have values equal to 0. WS annotations Group, UGA Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29 sequence alignment data set A data set that is produced as the output of some sequence alignment process. WS Annotations Group, UGA WS Annotations Group, UGA sequence alignment data format specification A data format specification that specifies the data format for the outcome of sequence alignment (pairwise or multiple) process. ITPPR Ready for OBI-WS : v1.0 ITPPR multiple sequence alignment data format specification WS Annotations Group, UGA 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 Ready for OBI-WS : v1.0 WS Annotations Group, UGA order of sequences in alignment setting specification order of sequences in alignment ClustalW Web service Documentation WS Annotations Group, UGA 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. web service execution status 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 ClustalW Web service Documentation www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa WS Annotations Group, UGA fast pairwise sequence alignment data transformation 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. are local, fast and slow pairwise alignments disjoint ITPPR ClustalW Documentation Ready for OBI-WS : v1.0 fast pairwise sequence alignment filter sequence data objective ITPPR ITPPR An objective specification that describes the goal of filtering sequence data depending on their similarity score to a specified sequence and expectation value. retrieve signal peptide result objective Assign IDs ITPPR 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. SignalP Web service documentation display multiple HSPs setting specification ITPPR FASTA Web service documentation 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. retrieve supported output data format objective ITPPR An objective specification that describes the goal of retrieving the supported output data formats for a particular web service execution. ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa base64 encoding 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://en.wikipedia.org/wiki/Base64 ITPPR protein signature recognition algorithm EBI online courses : http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/what-are-protein-signatures ITPPR An algorithm or a predictive model to predict the presence of a particular protein signature. assign ids retrieve web service execution result ITPPR get result ITPPR 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. signal peptide prediction score SignalP Web service documentation ITPPR A data item which is a score assigned for a signal peptide region predicted by a signal peptide prediction algorithm. signal peptide prediction threshold 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. SignalP Web service documentation ITPPR identify protein signature execution A web service execution that tries to locate occurrence of different known protein signatures like signal peptides in a protein sequence. ITPPR InterPro Documentation at EBI : ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/FAQs.html software execution setting specification ITPPR ITPPR 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. program setting parameter signal peptides prediction outcome SignalP Web service documentation / ITPPR 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. ITPPR comma separated values data format specification http://en.wikipedia.org/wiki/Comma-separated_values assign id ITPPR CSV data format A data format specification that consists of any number of records and each record separated by a comma (','). identify protein signature objective InterProScan Documentation at EBI ITPPR An objective specification that describes the goal of identifying protein signatures in a protein sequence. retrieve web service execution result objective assign id ITPPR ITPPR An objective specification that describes the goal of retrieving the outcome of some previously executed web service execution. predicted signal peptide cleavage sites data set ITPPR SignalP Web service documentation A predicted signal peptide cleavage sites data set that includes the outcome and all the meta data of signal peptide cleavage sites prediction process. phylip execution identifier ITPPR A web service execution identifier that uniquely identifies a submitted a phylip web service execution. Check how much it effect Suggestion..!! Obsolete it.! ITPPR construct phylogenetic trees objective http://en.wikipedia.org/wiki/Phylogenetic_tree#Unrooted_tree ITPPR A sequence analysis objective that describes the goal of constructing a phylogenetic tree that shows inferred evolutionary relationships between protein sequences. consensus tree construction algorithm An algorithm that is the method for construction of consensus tree. ITPPR ITPPR phylogenetic tree http://evolution.genetics.washington.edu/phylip/doc/neighbor.html 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. ITPPR evolution based amino acid substitution matrix ITPPR http://molecularevolution.org/resources/models/aa 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. compute protein evolution distance objective ITPPR 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://cmgm.stanford.edu/phylip/protdist.html#0 consensus tree ITPPR http://evolution.genetics.washington.edu/phylip/doc/consense.html A phylogenetic tree that is a cladogram which summarizes agreement between two or more phylogenetic trees. genetic code 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). ITPPR http://en.wikipedia.org/wiki/Genetic_code construct consensus tree execution 2 A phylip execution that constructs a consensus tree that summarizes the agreement between two or more phylogenetic trees. ITPPR http://evolution.genetics.washington.edu/phylip/doc/consense.html transcript sequence data A RNA sequence data that is about the primary structure of RNA sequence produced by transcription. ITPPR ITPPR Predicted RNA/mRNA Sequence (introns spliced out). minimum signalp D score setting specification 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). ITPPR ITPPR min sigp D score minimum signalp sum score setting specification 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. ITPPR ITPPR min sigp sum score minimum signalp probability setting specification A software execution setting specification that specifies the minimum value of signal probability from SignalP-HMM. ITPPR ITPPR min sigp signal probability any or all signalp setting specification A software execution setting specification that specifies Union or intersection of advanced parameters. ITPPR ITPPR find genes objective An objective specification of retrieving genes based on different parameters (e.g., gene locus tag, taxonomy or signal peptide etc.). ITPPR ITPPR find genes by taxonomy execution A web service execution that retrieves all genes of one or more species/organism(s). ITPPR ITPPR gene locus tag A CRID symbol that is systematically applied to every gene in a genome within the context of sequencing projects. Gene ID ITPPR EMBL-EBI RNA sequence data A sequence data that is about the primary structure of RNA. ITPPR ITPPR coding sequence data A sequence data that is about primary structure of coding sequence of DNA. Coding Sequence ITPPR ITPPR protein sequence length A data item that represents length of predicted protein sequence. ITPPR ITPPR Protein Length. find genes using signal peptide execution A web service execution that retrieves all genes that are predicted to encode a signal peptide. ITPPR ITPPR genomic location of gene ITPPR 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. CBIL-UPENN For a gene identified by gene locus tag TGME49_039250 the corresponsing genomic location of the gene would be TGME49_chrVI: 484,995 - 494,025 (-) where 484,995 is the starting position and 494,025 is the end position of the gene in the genome data. location text find genes by locus tag execution A web service execution that retrieves genes using list of comma separated gene locus tag. ITPPR ITPPR maximum isoelectric point setting secification A software execution setting specification that specifies the upper bound for the protein isoelectric point. ITPPR ITPPR maximum isoelectric point minimum number of predicted transmembrane domains setting specification A software execution setting specification that specifies the lower bound on number of predicted transmembrane domains a protein may have. ITPPR ITPPR minimum number of predicted transmembrane domains minimum isoelectric point setting specification A software execution setting specification that specifies the lower bound for the protein isoelectric point. ITPPR ITPPR minimum isoelectric point epitope confidence setting specification 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. ITPPR ITPPR The epitope confidence can be specified as High, Medium or Low. epitope confidence find genes by transmembrane domain execution A web service execution that retrieves all genes having number of predicted transmembrane domains in a range that user specify. ITPPR ITPPR find genes by transmembrane domain find genes with epitopes execution 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. ITPPR ITPPR find genes with epitopes find genes by molecular weight execution A web service execution that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify. ITPPR ITPPR find genes by molecular weight minimum molecular weight setting specification A software execution setting specification that specifies the minimum value for protein molecular weight. ITPPR ITPPR minimum molecular weight maximum molecular weight setting specification A software execution setting specification that specifies the maximum value for protein molecular weight. ITPPR ITPPR maximum molecular weight maximum number of predicted transmembrane domains setting specification A software execution setting specification that specifies the upper bound on number of predicted transmembrane domains a protein may have. ITPPR ITPPR maximum number of predicted transmembrane domains find genes by isoelectric point execution A web service execution that retrieves all genes whose protein product has an isoelectric point in a range that user specify. ITPPR ITPPR find genes by isoelectric point region primary structure of sequence macromolecule 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. region polypeptide 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. polypeptide polymer_attribute http://purl.obolibrary.org/obo/so.owl An attribute to describe the kind of biological sequence. example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. organizational term PERSON:Alan Ruttenberg term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI PAM BLOSUM62 20 absolute both percent BLASTp A BLAST algorithm that searches/aligns a protein query sequence against a protein database at a protein level. BLASTx A BLAST algorithm that searches/aligns a nucleotide query sequence against a protein database at a protein level. BLASTn A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level. FASTA aligned Poisson bottom input kap sump high seg+xnu tBLASTn A BLAST algorithm that searches/aligns a protein query sequence against a nucleotide database at a protein level. top low seg xnu medium tBLASTx A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a protein level. normal