webService.owl
type: Ontology
version info: Release v1.1
comment: This file is based on checkout of our SVN repository revision $Revision: 61 $
date: 2012-12-18
default language: en
creator: Akshay Choche
creator: Alok Dhamanaskar
subject: An ontology for the annotation of bioinformatics web services.
description: An ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.
contributor: Chaitanya Guttula
contributor: Chris Stoeckert
contributor: Jessie Kissinger
creator: Jie Zheng
contributor: John Miller
version IRI: webService.owl

Description
type: AnnotationProperty
comment: An account of the content of the resource.
description: 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
type: AnnotationProperty
editor note: 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.
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Coutot
editor preferred term: has_specified_input
definition: 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.
term editor: PERSON: Alan Ruttenberg
example of usage: see is_input_of example_of_usage
type: ObjectProperty
sub property of: has participant
domain: planned process

definition
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
editor preferred term: definition
has curation status: ready for release

editor note
type: AnnotationProperty
definition: 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.
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: editor note
has curation status: ready for release

has curation status
type: AnnotationProperty
definition source: OBI_0000281
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot
editor preferred term: has curation status

imported from
type: AnnotationProperty
definition: For external terms/classes, the ontology from which the term was imported
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Melanie Courtot
editor preferred term: imported from
has curation status: pending final vetting

definition source
type: AnnotationProperty
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: definition source
definition: 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
has curation status: ready for release

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user
term editor: PERSON:Alan Ruttenberg
editor preferred term: curator note
has curation status: ready for release

term editor
type: AnnotationProperty
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition: 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
term editor: PERSON:Daniel Schober
editor preferred term: term editor
has curation status: ready for release

has_specified_output
type: AnnotationProperty
term editor: PERSON: Bjoern Peters
term editor: PERSON: Larry Hunter
term editor: PERSON: Melanie Courtot
editor preferred term: has_specified_output
definition: 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.
term editor: PERSON: Alan Ruttenberg
type: ObjectProperty
sub property of: has participant
domain: planned process
inverse of: is_specified_output_of

alternative term
type: AnnotationProperty
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: alternative term
has curation status: pending final vetting

editor preferred term
type: AnnotationProperty
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term: editor preferred term
has curation status: ready for release

example of usage
type: AnnotationProperty
definition: 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
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
term editor: PERSON:Daniel Schober
editor preferred term: example
has curation status: ready for release

is part of
type: ObjectProperty
type: TransitiveProperty
editor note: 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
alternative term: part of
alternative term: part_of
domain: entity
range: entity
inverse of: has part
sub property of: is located in

has part
type: ObjectProperty
type: TransitiveProperty
alternative term: has_part

inheres in
type: ObjectProperty
type: FunctionalProperty
alternative term: inheres_in
range: independent continuant
domain: dependent continuant
inverse of: is bearer of
sub property of: s depends on

is bearer of
type: ObjectProperty
alternative term: bearer of
alternative term: bearer_of
domain: independent continuant
range: dependent continuant

is realized by
type: ObjectProperty
alternative term: realized by
alternative term: realized_by

realizes
type: ObjectProperty
domain: process
range: realizable entity
inverse of: is realized by

participates in
type: ObjectProperty
alternative term: participates_in

has participant
type: ObjectProperty
alternative term: has_participant
range: continuant
domain: process
inverse of: participates in
property chain axiom: realizes
property chain axiom: inheres in

is concretization of
type: ObjectProperty
alternative term: concretization of
alternative term: concretization_of
range: specifically dependent continuant
domain: generically dependent continuant

concretizes
type: ObjectProperty
domain: specifically dependent continuant
range: generically dependent continuant
inverse of: is concretization of

s depends on
type: ObjectProperty
alternative term: s_depends_on
range: independent continuant
domain: specifically dependent continuant

is located in
type: ObjectProperty
alternative term: located in
alternative term: located_in

is about
type: ObjectProperty
editor note: 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.
definition source: Smith, Ceusters, Ruttenberg, 2000 years of philosophy
example of usage: This document is about information artifacts and their representations
definition: is_about is a (currently) primitive relation that relates an information artifact to an entity.
term editor: person:Alan Ruttenberg
domain: information content entity
has curation status: pending final vetting

denotes
type: ObjectProperty
editor note: 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
example of usage: 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.
definition source: Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
definition: 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
term editor: person:Alan Ruttenberg
sub property of: is about

is_specified_input_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
editor preferred term: is_specified_input_of
definition: 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.
term editor: Alan Ruttenberg
example of usage: 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
sub property of: participates in
range: planned process
inverse of: has_specified_input

is_specified_output_of
type: ObjectProperty
term editor: PERSON:Bjoern Peters
editor preferred term: is_specified_output_of
definition: 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.
term editor: Alan Ruttenberg
sub property of: participates in
range: planned process

achieves_planned_objective
type: ObjectProperty
example of usage: A cell sorting process achieves the objective specification 'material separation objective'
term editor: BP, AR, PPPB branch
definition source: PPPB branch derived
definition: 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.
editor preferred term: achieves_planned_objective
curator note: modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
range: objective specification
domain: planned process

is_encoded_in
type: ObjectProperty
comment: SWO proposed relation, link data with data format specification, or software with program language
domain: information content entity
range: data format specification
sub property of: topObjectProperty

is_encoded_of
type: ObjectProperty
range: information content entity
domain: data format specification
inverse of: is_encoded_in
sub property of: topObjectProperty

is_executed_in
type: ObjectProperty
editor note: propose to deprecate
comment: algorithm/software is_executed_in information process
range: software execution
sub property of: topObjectProperty

is_executed_of
type: ObjectProperty
editor note: propose to deprecate
domain: software execution
inverse of: is_executed_in
sub property of: topObjectProperty

has_dimension
type: DatatypeProperty
domain: matrix
range: nonNegativeInteger

has_description
type: DatatypeProperty
domain: entity
range: string

has_value
type: DatatypeProperty
domain: matrix
range: double
range: float
range: integer

entity
type: Class
subclass of: Thing
editor preferred term: entity

continuant
type: Class
subclass of: entity
definition: 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.
example of usage: a heart
example of usage: a person
example of usage: a symphony orchestra
editor preferred term: continuant
alternative term: endurant
example of usage: the color of a tomato
example of usage: the disposition of blood to coagulate
example of usage: the lawn and atmosphere in front of our building
example of usage: the mass of a cloud

occurrent
type: Class
subclass of: entity
definition: An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
example of usage: a surgical operation as processual context for a nosocomical infection
editor preferred term: occurrent
alternative term: perdurant
example of usage: the life of an organism
example of usage: the most interesting part of Van Gogh's life
example of usage: the spatiotemporal context occupied by a process of cellular meiosis
example of usage: the spatiotemporal region occupied by the development of a cancer tumor

independent continuant
type: Class
subclass of: continuant
definition: A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a person
example of usage: a symphony orchestra
example of usage: an organism
editor preferred term: independent continuant
alternative term: substantial entity
example of usage: the bottom right portion of a human torso
example of usage: the lawn and atmosphere in front of our building

dependent continuant
type: Class
subclass of: continuant
definition: A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
editor preferred term: dependent continuant

process
type: Class
subclass of: occurrent
definition: A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
editor preferred term: process
example of usage: the life of an organism
example of usage: the process of cell-division
example of usage: the process of sleeping

realizable entity
type: Class
subclass of: specifically dependent continuant
definition: 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.
editor note: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
editor preferred term: realizable entity
example of usage: the disposition of blood to coagulate
example of usage: the disposition of metal to conduct electricity
example of usage: the function of the reproductive organs
example of usage: the role of being a doctor

quality
type: Class
subclass of: specifically dependent continuant
definition: A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
editor preferred term: quality
example of usage: the ambient temperature of air
example of usage: the circumference of a waist
example of usage: the color of a tomato
example of usage: the mass of a piece of gold
example of usage: the shape of a nose
example of usage: the weight of a chimpanzee

specifically dependent continuant
type: Class
subclass of: dependent continuant
definition: 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.
alternative term: mode
alternative term: property
editor preferred term: specifically dependent continuant
example of usage: the color of a tomato
example of usage: the disposition of fish to decay
example of usage: the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
example of usage: the liquidity of blood
example of usage: the mass of a cloud
example of usage: the role of being a doctor
example of usage: the smell of mozzarella
alternative term: trope

role
type: Class
subclass of: realizable entity
definition: 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.
editor preferred term: role
example of usage: the role of a biological grandfather as legal guardian in the context of a system of laws
example of usage: the role of a chemical compound in an experiment
example of usage: the role of a patient relative as defined by a hospital administrative form
example of usage: the role of a person as a surgeon
example of usage: the role of a student in a university
example of usage: the role of a woman as a legal mother in the context of system of laws
example of usage: the role of ingested matter in digestion

generically dependent continuant
type: Class
subclass of: dependent continuant
definition: 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.
example of usage: a certain PDF file that exists in different and in several hard drives
editor preferred term: generically dependent continuant

material entity
type: Class
subclass of: independent continuant
definition: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
editor note: Examples: collection of random bacteria, a chair, dorsal surface of the body
editor note: 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.
editor preferred term: material entity

deoxyribonucleic acids
type: Class
subclass of: nucleic acid
definition: High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
editor preferred term: deoxyribonucleic acids
imported from: chebi.owl

molecular entity
type: Class
subclass of: material entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
editor note: 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
editor preferred term: molecular entity
imported from: chebi.owl

nucleic acid
type: Class
subclass of: macromolecule
definition: 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.
editor preferred term: nucleic acid
imported from: chebi.owl

ribonucleic acids
type: Class
subclass of: nucleic acid
definition: Naturally occurring polyribonucleotides.
editor preferred term: ribonucleic acids
imported from: chebi.owl

amino acids
type: Class
subclass of: molecular entity
definition: Carboxylic acids containing one or more amino groups.
editor preferred term: amino acids
imported from: chebi.owl

macromolecule
type: Class
subclass of: molecular entity
definition: 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.
editor preferred term: macromolecule
alternative term: polymer
imported from: chebi.owl

objective specification
type: Class
subclass of: directive information entity
editor note: 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."
editor note: Answers the question, why did you do this experiment?
definition source: OBI Plan and Planned Process/Roles Branch
definition source: OBI_0000217
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Barry Smith
term editor: PERSON: Bjoern Peters
term editor: PERSON: Jennifer Fostel
definition: 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.
editor preferred term: objective specification
example of usage: purpose of a study; support of hypothesis, discovery of new information
has curation status: pending final vetting

action specification
type: Class
subclass of: directive information entity
term editor: Alan Ruttenberg
definition source: OBI Plan and Planned Process branch
example of usage: Pour the contents of flask 1 into flask 2
definition: a directive information entity that describes an action the bearer will take
has curation status: metadata incomplete

datum label
type: Class
subclass of: information content entity
curator note: 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.
definition: 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
term editor: GROUP: IAO
editor preferred term: datum label
editor note: http://www.golovchenko.org/cgi-bin/wnsearch#4n
has curation status: metadata incomplete

software
type: Class
subclass of: plan specification
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Melanie Courtot
definition: Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit.
editor note: see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
editor preferred term: software
has curation status: metadata complete

data item
type: Class
subclass of: information content entity
editor note: 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.
editor note: 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.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
editor note: 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
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Chris Stoeckert
term editor: PERSON: Jonathan Rees
definition: 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.
alternative term: data
editor preferred term: data item
has curation status: pending final vetting

symbol
type: Class
subclass of: information content entity
editor note: 20091104, MC: this needs work and will most probably change
term editor: PERSON: Jonathan Rees
definition: a smallish, word-like datum...
editor preferred term: symbol

information content entity
type: Class
subclass of: generically dependent continuant
subclass of: Restriction
  on property: is about
  some values from: entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
definition source: OBI_0000142
term editor: PERSON: Chris Stoeckert
definition: an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
editor preferred term: information content entity
editor note: 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.
has curation status: pending final vetting

directive information entity
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is about
  some values from: realizable entity
editor note: 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.
editor note: 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
definition: An information content entity whose concretizations indicate to their bearer how to realize them in a process.
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
editor note: 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
has curation status: metadata incomplete

algorithm
type: Class
subclass of: plan specification
definition: 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.
definition source: OBI_0000270
example of usage: PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
term editor: Philippe Rocca-Serra
term editor: PlanAndPlannedProcess Branch
definition source: adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
editor preferred term: algorithm
has curation status: metadata complete

curation status specification
type: Class
equivalent class: Class
  one of: uncurated
  one of: to be replaced with external ontology term
  one of: pending final vetting
  one of: ready for release
  one of: metadata incomplete
  one of: requires discussion
  one of: metadata complete
  one of: organizational term
  one of: example to be eventually removed
subclass of: data about an ontology part
editor note: Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
definition source: OBI_0000266
term editor: PERSON:Bill Bug
definition: 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.
editor preferred term: curation status specification
has curation status: pending final vetting

data format specification
type: Class
subclass of: directive information entity
editor note: 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"
definition: 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
definition source: OBI branch derived
definition source: OBI_0000187
term editor: PERSON: Alan Ruttenberg
term editor: PlanAndPlannedProcess Branch
editor preferred term: data format specification
has curation status: metadata incomplete

data set
type: Class
subclass of: data item
editor note: 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
definition: 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.
example of usage: Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
definition source: OBI_0000042
editor preferred term: data set
definition source: group:OBI
term editor: person:Allyson Lister
term editor: person:Chris Stoeckert
has curation status: metadata complete

data about an ontology part
type: Class
subclass of: data item
term editor: Person:Alan Ruttenberg
definition: data about an ontology part is a data item about a part of an ontology, for example a term

plan specification
type: Class
subclass of: directive information entity
subclass of: Restriction
  on property: has part
  some values from: action specification
subclass of: Restriction
  on property: has part
  some values from: objective specification
comment: 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
editor note: 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.
term editor: Alan Ruttenberg
editor note: Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
definition source: OBI Plan and Planned Process branch
definition source: OBI_0000344
example of usage: PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
definition: 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.
editor preferred term: plan specification
has curation status: metadata complete

measurement datum
type: Class
subclass of: data item
editor note: 2/2/2009 is_specified_output of some assay?
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
example of usage: 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,}.
definition source: OBI_0000305
definition source: group:OBI
editor preferred term: measurement datum
term editor: person:Chris Stoeckert
has curation status: metadata complete

textual entity
type: Class
subclass of: information content entity
definition: 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.
editor note: 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.
editor note: 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.
term editor: PERSON: Lawrence Hunter
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
alternative term: text
editor preferred term: textual entity

document
type: Class
subclass of: information content entity
definition: A collection of information content entities intended to be understood together as a whole
example of usage: A journal article, patent application, laboratory notebook, or a book
term editor: PERSON: Lawrence Hunter
editor preferred term: document
has curation status: metadata complete

email address
type: Class
subclass of: information content entity
editor note: 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
term editor: Person:Alan Ruttenberg
term editor: Person:Chris Stoeckart
editor preferred term: email address
has curation status: metadata incomplete

CRID symbol
type: Class
subclass of: symbol
definition: A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
editor note: 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.
definition source: Original proposal from Bjoern, discussions at IAO calls
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bill Hogan
term editor: PERSON: Bjoern Peters
term editor: PERSON: Melanie Courtot
example of usage: PMID:12345, 12345 in a database column which has header "pubmedID"

Viruses
type: Class
subclass of: organism
editor preferred term: Viruses
imported from: ncbitaxon.owl

Teleostomi
type: Class
subclass of: Gnathostomata
editor preferred term: Teleostomi
imported from: ncbitaxon.owl

Euteleostomi
type: Class
subclass of: Teleostomi
editor preferred term: Euteleostomi
imported from: ncbitaxon.owl

Bacteria
type: Class
subclass of: organism
editor preferred term: Bacteria
imported from: ncbitaxon.owl

Homo/Pan/Gorilla group
type: Class
subclass of: Hominidae
editor preferred term: Homo/Pan/Gorilla group
imported from: ncbitaxon.owl

Archaea
type: Class
subclass of: organism
editor preferred term: Archaea
imported from: ncbitaxon.owl

Eukaryota
type: Class
subclass of: organism
editor preferred term: Eukaryota
imported from: ncbitaxon.owl

Euarchontoglires
type: Class
subclass of: Eutheria
editor preferred term: Euarchontoglires
imported from: ncbitaxon.owl

Simiiformes
type: Class
subclass of: Haplorrhini
editor preferred term: Simiiformes
imported from: ncbitaxon.owl

Hominoidea
type: Class
subclass of: Catarrhini
editor preferred term: Hominoidea
imported from: ncbitaxon.owl

Tetrapoda
type: Class
subclass of: Sarcopterygii
editor preferred term: Tetrapoda
imported from: ncbitaxon.owl

Amniota
type: Class
subclass of: Tetrapoda
editor preferred term: Amniota
imported from: ncbitaxon.owl

Theria
type: Class
subclass of: Mammalia
editor preferred term: Theria
imported from: ncbitaxon.owl

Fungi/Metazoa group
type: Class
subclass of: Eukaryota
editor preferred term: Fungi/Metazoa group
imported from: ncbitaxon.owl

Metazoa
type: Class
subclass of: Fungi/Metazoa group
editor preferred term: Metazoa
imported from: ncbitaxon.owl

Bilateria
type: Class
subclass of: Eumetazoa
editor preferred term: Bilateria
imported from: ncbitaxon.owl

Coelomata
type: Class
subclass of: Bilateria
editor preferred term: Coelomata
imported from: ncbitaxon.owl

Deuterostomia
type: Class
subclass of: Coelomata
editor preferred term: Deuterostomia
imported from: ncbitaxon.owl

Haplorrhini
type: Class
subclass of: Primates
editor preferred term: Haplorrhini
imported from: ncbitaxon.owl

Mammalia
type: Class
subclass of: Amniota
editor preferred term: Mammalia
imported from: ncbitaxon.owl

Eumetazoa
type: Class
subclass of: Metazoa
editor preferred term: Eumetazoa
imported from: ncbitaxon.owl

Chordata
type: Class
subclass of: Deuterostomia
editor preferred term: Chordata
imported from: ncbitaxon.owl

Vertebrata
type: Class
subclass of: Craniata
editor preferred term: Vertebrata
imported from: ncbitaxon.owl

Gnathostomata
type: Class
subclass of: Vertebrata
editor preferred term: Gnathostomata
imported from: ncbitaxon.owl

Sarcopterygii
type: Class
subclass of: Euteleostomi
editor preferred term: Sarcopterygii
imported from: ncbitaxon.owl

Craniata
type: Class
subclass of: Chordata
editor preferred term: Craniata
imported from: ncbitaxon.owl

Eutheria
type: Class
subclass of: Theria
editor preferred term: Eutheria
imported from: ncbitaxon.owl

Primates
type: Class
subclass of: Euarchontoglires
editor preferred term: Primates
imported from: ncbitaxon.owl

Catarrhini
type: Class
subclass of: Simiiformes
editor preferred term: Catarrhini
imported from: ncbitaxon.owl

Hominidae
type: Class
subclass of: Hominoidea
editor preferred term: Hominidae
imported from: ncbitaxon.owl

Homo
type: Class
subclass of: Homo/Pan/Gorilla group
editor preferred term: Homo
imported from: ncbitaxon.owl

Homo sapiens
type: Class
subclass of: Homo
alternative term: human being
editor preferred term: Homo sapiens
imported from: ncbitaxon.owl

planned process
type: Class
equivalent class: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: Class
      intersection of: plan specification
      intersection of: Restriction
        on property: has part
        some values from: objective specification
subclass of: process
editor note: '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.)
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
term editor: Bjoern Peters
example of usage: Injecting mice with a vaccine in order to test its efficacy
editor note: 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.
definition source: branch derived
definition: A processual entity that realizes a plan which is the concretization of a plan specification.
curator note: 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)
editor preferred term: planned process
has curation status: ready for release

quantitative confidence value
type: Class
subclass of: data item
definition source: group:OBI
definition: A data item which is used to indicate the degree of uncertainty about a measurement.
term editor: person:Chris Stoeckert
editor preferred term: quantitative confidence value
has curation status: pending final vetting

organization
type: Class
subclass of: material entity
definition source: GROUP: OBI
term editor: PERSON: Alan Ruttenberg
term editor: PERSON: Bjoern Peters
term editor: PERSON: Philippe Rocca-Serra
term editor: PERSON: Susanna Sansone
definition: 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.
editor note: 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.
example of usage: 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.
editor preferred term: organization
has curation status: ready for release

primary structure of DNA macromolecule
type: Class
equivalent class: Restriction
  on property: is concretization of
  some values from: Restriction
    on property: inheres in
    some values from: deoxyribonucleic acids
subclass of: region
term editor: BP et al
definition: a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
editor note: placeholder for SO
editor preferred term: primary structure of DNA macromolecule
has curation status: metadata incomplete

primary structure of RNA molecule
type: Class
equivalent class: Restriction
  on property: is concretization of
  some values from: Restriction
    on property: inheres in
    some values from: ribonucleic acids
subclass of: region
term editor: Person:Bjoern Peters
definition: 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
editor preferred term: primary structure of RNA molecule
has curation status: metadata incomplete

record of missing knowledge
type: Class
subclass of: information content entity
example of usage: 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.
term editor: Bjoern Peters
editor note: 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.
definition: a information content entity created to indicate that information about something is not available to the person recording it.
editor preferred term: record of missing knowledge
has curation status: metadata complete

service consumer role
type: Class
subclass of: role
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
example of usage: A biologist who uses a sequencing services fulfills the role of a service consumer
definition source: OBI
term editor: Person:Helen Parkinson
definition: a role which inheres in a person who uses a service
editor preferred term: service consumer role
has curation status: metadata complete

service provider role
type: Class
subclass of: role
subclass of: Restriction
  on property: is realized by
  all values from: planned process
subclass of: Restriction
  on property: inheres in
  some values from: Class
    union of: Homo sapiens
    union of: organization
example of usage: Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
term editor: PERSON:Helen Parkinson
definition: 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
editor preferred term: service provider role
has curation status: metadata incomplete

sequence data
type: Class
subclass of: measurement datum
subclass of: Class
  intersection of: measurement datum
  intersection of: Restriction
    on property: is about
    some values from: region
definition: A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
definition source: GROUP: OBI
term editor: Person:Chris Stoeckert
example of usage: example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
editor preferred term: sequence data
has curation status: metadata complete

service
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Class
    intersection of: Restriction
      on property: realizes
      some values from: service consumer role
    intersection of: Restriction
      on property: realizes
      some values from: service provider role
subclass of: planned process
subclass of: Restriction
  on property: has part
  some values from: planned process
definition: A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
term editor: Carlo; Matt
definition source: OBI workshop San Diego 2011
example of usage: 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
editor preferred term: service
has curation status: metadata complete

DNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
curator note: 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.
definition: A sequence data item that is about the primary structure of DNA
editor preferred term: DNA sequence data
term editor: OBI call; Bjoern Peters
definition source: OBI call; Melanie Courtout
example of usage: The part of a FASTA file that contains the letters ACTGGGAA
has curation status: metadata complete

organism
type: Class
equivalent class: Class
  union of: Viruses
  union of: Bacteria
  union of: Archaea
  union of: Eukaryota
subclass of: material entity
editor note: 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')
editor note: 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.
term editor: GROUP: OBI Biomaterial Branch
definition: 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.
definition source: WEB: http://en.wikipedia.org/wiki/Organism
example of usage: animal
example of usage: fungus
editor preferred term: organism
example of usage: plant
example of usage: virus
has curation status: organizational term

data transformation
type: Class
subclass of: planned process
subclass of: Restriction
  on property: has_specified_output
  some values from: data item
subclass of: Restriction
  on property: has_specified_input
  some values from: data item
subclass of: Restriction
  on property: has_specified_output
  all values from: data item
subclass of: Restriction
  on property: has_specified_input
  all values from: data item
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: data transformation objective
term editor: Philippe Rocca-Serra
example of usage: 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.
definition: A data transformation is a process which produces output data from input data
definition source: Branch editors
term editor: Elisabetta Manduchi
term editor: Helen Parkinson
term editor: James Malone
term editor: Melanie Courtot
term editor: Richard Scheuermann
term editor: Ryan Brinkman
term editor: Tina Hernandez-Boussard
alternative term: data analysis
alternative term: data processing
editor preferred term: data transformation
has curation status: pending final vetting

sequence analysis objective
type: Class
subclass of: data transformation objective
term editor: James Malone
definition source: PERSON: James Malone
definition: A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
editor preferred term: sequence analysis objective
has curation status: metadata complete

data transformation objective
type: Class
subclass of: objective specification
definition: A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
term editor: James Malone
definition source: PERSON: James Malone
editor preferred term: data transformation objective
example of usage: normalize objective
has curation status: ready for release

digital document name
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: denotes
  some values from: document
term editor: ITPPR
definition: A textual entity that refers to a digital document derived from a computer system.
definition source: ITPPR
alternative term: file name

file extension
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is part of
  all values from: digital document name
definition: A textual entity that is the suffix for a file name.
definition source: EDAM: file extension
term editor: WS annotations Group, UGA

metadata of data format specification
type: Class
subclass of: digital document name
subclass of: Restriction
  on property: is about
  some values from: data format specification
subclass of: Restriction
  on property: has part
  some values from: data format specification identifier
subclass of: Restriction
  on property: has part
  some values from: file extension
subclass of: Restriction
  on property: has part
  some values from: datum label
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: denotes
    some values from: MIME type specification
definition: A textual entity that gives the details of the different supported data formats and associated file extension and other metadata.
term editor: WS annotations Group, UGA
definition source: ClustalW Web service Documentation

MIME type specification
type: Class
subclass of: data format specification
definition: A data format specification that is used to specify the content type over the Web. (MIME is an acronym for Multipurpose Internet Mail Extension)
editor note: Ready for OBI-WS : v1.0
definition source: Wikipedia: en.wikipedia.org/wiki/MIME
term editor: WS Annotations Group, UGA

clustering algorithm
type: Class
subclass of: algorithm
term editor: WS Annotations Group, UGA
editor note: Ready for OBI-WS : v1.0
definition: 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.
definition source: Wikipedia: en.wikipedia.org/wiki/Nearest_neighbor_search

sequence similarity identification objective
type: Class
subclass of: sequence analysis objective
definition: A sequence analysis objective that describes the aim to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
term editor: ITPPR
definition source: EDAM: alignment
editor note: Ready for OBI-WS : v1.0

pairwise sequence alignment algorithm
type: Class
subclass of: algorithm
subclass of: Restriction
  on property: has part
  some values from: pairwise sequence alignment objective
subclass of: Restriction
  on property: is_executed_in
  some values from: pairwise sequence alignment data transformation
definition: An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences).
definition source: WS Annotations Group, UGA
term editor: WS Annotations Group, UGA
editor note: Ready for OBI-WS : v1.0

multiple sequence alignment algorithm
type: Class
subclass of: algorithm
subclass of: Restriction
  on property: has part
  some values from: multiple sequence alignment objective
definition: An algorithm that is used to obtain multiple sequence alignments between nucleotide or protein sequences.
editor note: Ready for OBI-WS : v1.0
term editor: ITPPR
definition source: ITPPR

gap separation distance setting specification
type: Class
subclass of: software execution setting specification
definition source: ClustalW Web service Documentation and WS annotations Group, UGA
definition: 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.
term editor: WS Annotations Group, UGA
alternative term: gap separation distance

end gap separation penalty setting specification
type: Class
subclass of: software execution setting specification
description: 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.
term editor: WS Annotations Group, UGA
alternative term: end gap separation penalty
definition source: ClustalW Web service Documentation and WS annotations Group, UGA
definition: 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
type: Class
subclass of: software execution setting specification
alternative term: number of iterations
definition source: ClustalW Web service Documentation
has curation status: WS Annotations Group, UGA
definition: A software execution setting specification that specifies the maximum number of iterations to perform.

iteration strategy setting specification
type: Class
subclass of: software execution setting specification
definition source: ClustalW Web service Documentation
alternative term: iteration strategy
term editor: WS Annotations Group, UGA
definition: 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
type: Class
subclass of: symbol
subclass of: Restriction
  on property: denotes
  some values from: algorithm
term editor: ITPPR
definition source: ITPPR
definition: A symbol that specifies a particular algorithm to be implemented in a tool or software.

multiple sequence alignment guide tree
type: Class
subclass of: data set
definition: 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.
definition source: Wikipedia : http://en.wikipedia.org/wiki/Multiple_sequence_alignment
term editor: ITPPR

retrieve alignment result objective
type: Class
subclass of: retrieve web service execution result objective
definition source: ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
definition: A retrieve web service execution result objective that describes the goal of retrieving the sequence alignment result.
editor note: Ready for OBI-WS : v1.0
term editor: WS Annotations Group, UGA

web service execution identifier
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: denotes
  all values from: web service execution
editor note: Unique identifier for Web Service job
alternative term: job id
definition: A CRID symbol used to uniquely identify a submitted web service execution.
term editor: ITPPR
definition source: ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa

multiple sequence alignment data set
type: Class
subclass of: sequence alignment data set
subclass of: Restriction
  on property: is_specified_output_of
  some values from: Class
    intersection of: planned process
    intersection of: Restriction
      on property: achieves_planned_objective
      some values from: multiple sequence alignment objective
term editor: WS Annotations Group, UGA
definition: A sequence alignment data set that is produced as the output of a multiple sequence alignment process.
definition source: WS Annotations Group, UGA

web service execution title
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: denotes
  all values from: web service execution
alternative term: job title
definition source: ClustalW Web service Documentation
definition: A textual entity that is the name of a web service job submitted.
term editor: ITPPR

filter sequence data
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: filter sequence data objective
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence similarity expectation value
subclass of: Restriction
  on property: has_specified_output
  some values from: sequence data
definition: A web service execution that filters sequence data depending on their similarity score to a specified sequence and expectation value.
term editor: ITPPR
definition source: ITPPR

gap creation penalty setting specification
type: Class
subclass of: gap penalty setting specification
definition: A gap penalty setting specification that specifies the penalty for introducing a new gap when producing an alignment.
alternative term: gap creation penalty
definition source: EDAM: gap creation penalty
term editor: WS Annotations Group, UGA

DNA substitution matrix
type: Class
subclass of: scoring matrix
definition: A scoring matrix that is used for scoring alignment of nucleotide sequences.
term editor: WS annotations Group, UGA
definition source: WS annotations Group, UGA

protein distance matrix
type: Class
subclass of: matrix
definition: 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.
term editor: WS annotations Group, UGA
definition source: http://cmgm.stanford.edu/phylip/protdist.html

compute protein evolution distance execution
type: Class
subclass of: phylip execution
subclass of: Restriction
  on property: has_specified_input
  some values from: evolution based amino acid substitution matrix
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: compute protein evolution distance objective
subclass of: Restriction
  on property: has_specified_input
  some values from: multiple sequence alignment data set
definition: A phylip execution that computes a protein evolution distance matrix using a amino acid replacement model.
term editor: ITPPR
definition source: http://cmgm.stanford.edu/phylip/protdist.html#0

gap extension penalty setting specification
type: Class
subclass of: gap penalty setting specification
editor note: Ready for OBI-WS : v1.0
alternative term: gap extension penalty
term editor: WS Annotations Group, UGA
definition source: EDAM: gap extension penalty
definition: A gap penalty setting specification that specifies the penalty for extending a gap when aligning sequences.

construct phylip neighbor tree execution
type: Class
subclass of: phylip execution
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: construct phylogenetic trees objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: is about
      all values from: clustering algorithm
subclass of: Restriction
  on property: has_specified_input
  some values from: protein distance matrix
definition: 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.
term editor: ITPPR
definition source: http://evolution.genetics.washington.edu/phylip/doc/neighbor.html

phylip execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  all values from: phylip execution identifier
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: sequence analysis objective
definition: A web service execution that involves invocation of different programs for inferring phylogenetic relationships between groups of organisms.
definition source: http://en.wikipedia.org/wiki/Phylogenetics, http://www.phylip.com/
term editor: ITPPR

get web service execution status
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  all values from: web service execution identifier
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: check web service execution status objective
subclass of: Restriction
  on property: has_specified_output
  all values from: web service execution status
term editor: ITPPR
definition: A web service execution that returns the status (e.g. Finished, Running) of a web service execution, depending upon web service execution identifier. .
definition source: ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
alternative term: get job status

clustalW execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: web service execution title
subclass of: Restriction
  on property: has_specified_input
  some values from: order of sequences in alignment setting specification
subclass of: Restriction
  on property: has_specified_output
  all values from: web service execution identifier
subclass of: Restriction
  on property: has_specified_input
  some values from: multiple sequence alignment data format specification
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: denotes
      some values from: pairwise sequence alignment algorithm
subclass of: Restriction
  on property: has part
  some values from: pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: email address
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      all values from: polymer_attribute
subclass of: Restriction
  on property: has part
  some values from: multiple sequence alignment data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple sequence alignment objective
definition source: ClustalW Web service Documentation
definition: A web service execution that performs multiple sequence alignment.
term editor: ITPPR

get supported output data format
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  some values from: metadata of data format specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: retrieve supported output data format objective
subclass of: Restriction
  on property: has_specified_input
  all values from: web service execution identifier
definition: A web service execution that retrieves all the supported output data format for a particular execution.
term editor: ITPPR
definition source: ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
alternative term: get result types

retrieve alignment result execution
type: Class
subclass of: retrieve web service execution result
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: retrieve alignment result objective
subclass of: Restriction
  on property: has_specified_output
  all values from: Class
    intersection of: multiple sequence alignment data set
    intersection of: Restriction
      on property: is_encoded_in
      some values from: Class
        intersection of: data format specification
        intersection of: Restriction
subclass of: Restriction
  on property: has_specified_input
  some values from: data format specification
subclass of: Restriction
  on property: has_specified_input
  all values from: web service execution identifier
definition source: ClustalW Web service Documentation
term editor: WS annotations Group, UGA
definition: A retrieve web service execution result that would fetch the result of alignment analysis given its unique execution identifier.

web service
type: Class
subclass of: service
subclass of: Restriction
  on property: has part
  some values from: web service execution
definition: 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.
definition source: Wikipedia: http://en.wikipedia.org/wiki/Web_service
term editor: ITPPR

amino acid substitution matrix
type: Class
subclass of: scoring matrix
example of usage: 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.
term editor: WS annotations Group, UGA
definition source: http://en.wikipedia.org/wiki/Substitution_matrix
definition: 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
type: Class
equivalent class: Class
  intersection of: planned process
  intersection of: Restriction
    on property: realizes
    some values from: Restriction
      on property: concretizes
      some values from: software
subclass of: planned process
subclass of: Restriction
  on property: achieves_planned_objective
  all values from: objective specification
subclass of: Restriction
  on property: has_specified_input
  all values from: information content entity
subclass of: Restriction
  on property: has_specified_output
  all values from: information content entity
definition source: ITPPR
term editor: ITPPR
alternative term: operation
definition: A planned process that realizes the concretization of a software.

scoring matrix
type: Class
subclass of: lower triangular matrix
definition: 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.
term editor: WS annotations Group, UGA
definition source: WS annotations Group, UGA

gap penalty setting specification
type: Class
subclass of: software execution setting specification
term editor: WS Annotations Group, UGA
definition source: EDAM: gap Penalty
alternative term: gap penalty
definition: 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
type: Class
subclass of: objective specification
definition source: ITPPR
term editor: ITPPR
definition: An objective specification that a web service execution accomplishes.
editor note: Ready for OBI-WS : v1.0

number of match regions setting specification
type: Class
subclass of: software execution setting specification
alternative term: number of matched regions
definition: 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.
definition source: ClustalW Web service Documentation
term editor: WS Annotations Group, UGA

fast pairwise alignment scoring method setting specification
type: Class
subclass of: software execution setting specification
subclass of: Restriction
  on property: is about
  some values from: fast pairwise sequence alignment data transformation
definition source: ClustalW Web service Documentation
definition: A software execution setting specification that specifies the output type for fast pairwise alignment score (can be either percent or absolute).
term editor: WS Annotations Group, UGA
alternative term: fast pairwise alignment scoring method

alignment window size setting specification
type: Class
subclass of: software execution setting specification
term editor: WS Annotations Group, UGA
alternative term: alignment window size
definition source: ClustalW Web service Documentation
definition: 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
type: Class
subclass of: software execution setting specification
definition source: ClustalW Web service Documentation
term editor: WS Annotations Group, UGA
alternative term: alignment word size
definition: 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
type: Class
subclass of: sequence similarity identification objective
definition: A sequence similarity identification objective that aims to align multiple sequences at a time to determine the equivalence between them.
editor note: Ready for OBI-WS : v1.0
term editor: ITPPR
definition source: EDAM: alignment & ITPPR

pairwise sequence alignment objective
type: Class
subclass of: sequence similarity identification objective
definition: A sequence similarity identification objective that aims to align two sequences at a time to determine the equivalence between them.
term editor: WS Annotations Group, UGA
definition source: WS Annotations Group, UGA
editor note: Ready for OBI-WS : v1.0

number of top combinations setting specification
type: Class
subclass of: software execution setting specification
definition: 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'
term editor: ITPPR
definition source: WU-Blast Web service documentation
alternative term: number of top combinations

pairwise alignment sensitivity setting specification
type: Class
subclass of: software execution setting specification
definition: 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).
term editor: ITPPR
definition source: WU-Blast Web service documentation
alternative term: pairwise alignment sensitivity

pairwise alignment statistical model setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies a statistical model to use for scoring alignments (pairwise). Can take values from (sum p, Poisson, kap).
definition source: WU-BLAST Web service documentation
term editor: ITPPR
alternative term: pairwise alignment statistical model

pairwise alignment data format specification
type: Class
subclass of: sequence alignment data format specification
definition: A data format specification that specifies the format for the data produced as a result of pairwise sequence alignment. e.g. BLASTXML
editor note: Ready for OBI-WS : v1.0
definition source: WUBlast Web service documentation
term editor: ITPPR

low complexity sequence filter algorithm identifier
type: Class
subclass of: sequence filter algorithm identifier
definition: 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.
definition source: http://www.ebi.ac.uk/Tools/sss/wublast/help/index-protein.html#filter
term editor: ITPPR

sequence filter algorithm identifier
type: Class
subclass of: algorithm identifier
definition: A data item which specifies a sequence filter that pre-processes the query sequence before alignment to remove the undesired portions of it.
definition source: WU-BLAST Web service documentation
term editor: ITPPR

inclusion of filtered sequences setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
definition source: WU-BLAST Web service documentation
alternative term: inclusion of filtered sequences
term editor: ITPPR

maximum match score setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the maximum number of match scores displayed in the output.
term editor: ITPPR
alternative term: maximum match score
definition source: WU-BLAST Web service documentation

sequence range setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that defines the range of query sequence to use for search.
term editor: ITPPR
alternative term: sequence range
editor note: NCBI BLAST Web service documentation

maximum number of matched alignments setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the maximum number of alignments displayed in the output.
definition source: WU-BLAST Web service documentation
alternative term: maximum number of matched alignment
term editor: ITPPR

gene strand specifier
type: Class
subclass of: textual entity
definition: A textual entity that specifies the DNA strand, upper, lower or both of a specific gene to be considered in alignment.
term editor: ITPPR
definition source: WU-BLAST Web service documentation

drop-off score setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
term editor: ITPPR
alternative term: drop-off score
definition source: NCBI BLAST Web service documentation

sequence database for similarity search
type: Class
subclass of: data set
definition: A data set that is stored on a computer and used for molecular sequence similarity search.
definition source: WEBSITE:http://en.wikipedia.org/wiki/Sequence_database
term editor: ITPPR

pairwise alignment hits ordering setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
definition source: WU-BLAST Web service documentation
alternative term: pairwise alignment hits ordering
term editor: ITPPR

protein sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: polypeptide
definition source: OBI / ITPPR
definition: A sequence data that is about sequence of amino acids which are linked by peptide bonds.
term editor: ITPPR

data format specification identifier
type: Class
subclass of: symbol
subclass of: Restriction
  on property: denotes
  some values from: data format specification
definition: A symbol used to identify (uniquely for a particular web service) the output type.
alternative term: result type identifier
definition: WS annotations Group, UGA
term editor: WS annotations Group, UGA

sequence similarity expectation value
type: Class
subclass of: quantitative confidence value
definition: A quantitative confidence value which determines a threshold value such that only alignments scoring more than this value are considered.
alternative term: expectation value
definition source: WUBlast Web service documentation
term editor: ITPPR

retrieve signal peptide result
type: Class
subclass of: retrieve web service execution result
subclass of: Restriction
  on property: has_specified_input
  some values from: web service execution identifier
subclass of: Restriction
  on property: has_specified_output
  some values from: predicted signal peptide cleavage sites data set
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: retrieve signal peptide result objective
term editor: ITPPR
definition source: SignalP Web service documentation
definition: 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
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: data item
    intersection of: Restriction
      on property: is about
      all values from: polymer_attribute
subclass of: Restriction
  on property: has_specified_input
  some values from: gene strand specifier
subclass of: Restriction
  on property: has_specified_input
  some values from: maximum match score setting specification
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: pairwise sequence alignment objective
subclass of: Restriction
  on property: has_specified_input
  some values from: match mismatch scores setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: pairwise alignment sensitivity setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence database for similarity search
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence range setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: email address
subclass of: Restriction
  on property: has_specified_input
  some values from: pairwise alignment hits ordering setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: pairwise alignment statistical model setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: algorithm identifier
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence similarity expectation value
subclass of: Restriction
  on property: has_specified_input
  some values from: gap extension penalty setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: web service execution identifier
subclass of: Restriction
  on property: has_specified_input
  some values from: gaps alignment setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: inclusion of filtered sequences setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: gap creation penalty setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: pairwise alignment data format specification
subclass of: Restriction
  on property: has_specified_input
  some values from: scoring matrix
subclass of: Restriction
  on property: has_specified_input
  some values from: web service execution title
subclass of: Restriction
  on property: has_specified_input
  some values from: number of top combinations setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: drop-off score setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: maximum number of matched alignments setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: low complexity sequence filter algorithm identifier
definition: A web service execution that performs local pairwise sequence alignment to search a database for similar sequences.
definition source: ITPPR
term editor: ITPPR
editor note: It is getting inferred as a Sequence alignment data Transformation is that what we want

signal peptide prediction algorithm
type: Class
subclass of: protein signature recognition algorithm
definition source: SignalP Web service documentation
definition: A protein signature prediction method that serves as a prediction model to predict the location of signal peptides in a protein sequence.
term editor: ITPPR

predicted protein signatures data set
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: sequence range setting specification
subclass of: Restriction
  on property: has part
  some values from: sequence data
term editor: ITPPR
definition source: InterProScan Documentation
definition: A data set that is as an outcome of protein signature prediction process.

BLAST algorithm
type: Class
subclass of: pairwise sequence alignment algorithm
subclass of: Restriction
  on property: is_executed_in
  some values from: BLAST analysis data transformation
definition: 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.
definition source: Wikipedia: BLAST
editor note: Ready for OBI-WS : v1.0
term editor: ITPPR

pairwise sequence alignment data transformation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: pairwise sequence alignment objective
definition: 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.
editor note: Ready for OBI-WS : v1.0
definition source: EDAM: alignment & WS Annotations Group, UGA
term editor: ITPPR
alternative term: pairwise sequence alignment

local pairwise sequence alignment data transformation
type: Class
subclass of: pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data
definition: 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.
alternative term: local pairwise sequence alignment
term editor: ITPPR
editor note: Ready for OBI-WS : v1.0
definition source: EDAM: alignment & WS Annotations Group, UGA

global multiple sequence alignment data transformation
type: Class
subclass of: multiple sequence alignment data transformation
definition: A multiple sequence alignment data transformation that attempts to align the sequences considering their entire length.
definition source: WS Annotations Group, UGA
alternative term: global multiple sequence alignment
editor note: Ready for OBI-WS : v1.0
has curation status: ITPPR

check web service execution status objective
type: Class
subclass of: objective specification
definition: An objective specification that describes the goal of fetching the status of a web service execution.
editor note: Ready for OBI-WS : v1.0
term editor: ITPPR
alternative term: check job status objective

record of missing annotation
type: Class
subclass of: record of missing knowledge
definition: A record of missing knowledge that describes terms in the document that are not present in the ontology.
alternative term: unannotated term
definition source: WS Annotations Group, UGA
term editor: ITPPR

match mismatch scores setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the scores for a match and miss-match, to be used when searching for similar nucleotide sequences.
definition source: NCBI BLAST Web service documentation
term editor: ITPPR
alternative term: match mismatch scores

BLAST analysis data transformation
type: Class
subclass of: local pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence database for similarity search
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: BLAST algorithm
definition: A local pairwise sequence alignment data transformation that performs pairwise sequence alignment to search sequence databases for similar sequences.
alternative term: BLAST analysis
term editor: WS Annotations Group, UGA
definition source: Documentation for BLAST at NCBI
editor note: Ready for OBI-WS : v1.0

sequence identifier
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: denotes
  some values from: sequence data
definition: A CRID symbol that serves as an identifier for a molecular sequence or for an entry from a molecular sequence database.
definition source: EDAM: sequence identifier
term editor: ITPPR

gaps alignment setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
term editor: ITPPR
definition source: NCBIBlast Web service documentation
alternative term: gaps alignment

matrix
type: Class
subclass of: data set
term editor: WS annotations Group, UGA
definition source: Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29
definition: A data set that is made up of a rectangular array of elements (or entries) set out by rows and columns.

fetch sequences execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: MIME type specification
subclass of: Restriction
  on property: has_specified_output
  some values from: sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence identifier
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence database for similarity search
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: fetch sequences objective
subclass of: Restriction
  on property: has_specified_input
  some values from: sequence data format specification
definition: A web service execution that retrieves the sequence given the sequence identifier and the sequence database that has the sequence.
term editor: ITPPR
definition source: ITPPR

predict signal peptides
type: Class
subclass of: identify protein signature execution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: is about
      all values from: signal peptide prediction algorithm
subclass of: Restriction
  on property: has_specified_output
  some values from: predicted signal peptide cleavage sites data set
subclass of: Restriction
  on property: has_specified_input
  some values from: signal peptide prediction threshold value
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: predict signal peptide cleavage sites objective
definition: An identify protein signature execution that attempts to predict the presence and location of signal peptide cleavage sites in a protein sequence.
definition source: SignalP Web service documentation
term editor: ITPPR

predict signal peptide cleavage sites objective
type: Class
subclass of: identify protein signature objective
definition: 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.
term editor: ITPPR
editor note: Ready for OBI-WS : v1.0
definition source: SignalP Web service documentation

web service execution
type: Class
subclass of: software execution
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: invoke software execution over network objective
definition: A software execution that is provided by the web service, and involves invoking software execution over network.
definition source: ITPPR
term editor: ITPPR
alternative term: web service operation

sequence data format specification
type: Class
subclass of: data format specification
definition: A data format specification for molecular sequence feature information.
definition source: EDAM
alternative term: sequence data format
term editor: ITPPR
editor note: Ready for OBI-WS : v1.0

fetch sequences objective
type: Class
subclass of: objective specification
definition: An objective specification of retrieving a sequence from a sequence database given the sequence identifier and the database that has the sequence.
alternative term: retrieve sequences objective
definition source: ITPPR
editor note: Ready for OBI-WS : v1.0
term editor: ITPPR

display histograms setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
alternative term: display histograms
definition source: FASTA Web service documentation

slow pairwise sequence alignment data transformation
type: Class
subclass of: pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: gap creation penalty setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: gap extension penalty setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: DNA substitution matrix
    union of: amino acid substitution matrix
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: pairwise sequence alignment objective
definition: 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.
editor note: Ready for OBI-WS : v1.0
definition source: ClustalW Documentation
term editor: ITPPR
alternative term: slow pairwise sequence alignment

multiple sequence alignment data transformation
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    union of: DNA substitution matrix
    union of: amino acid substitution matrix
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: is about
      all values from: clustering algorithm
subclass of: Restriction
  on property: has part
  some values from: Class
    union of: slow pairwise sequence alignment data transformation
    union of: fast pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: number of iterations setting specification
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: multiple sequence alignment algorithm
subclass of: Restriction
  on property: has_specified_input
  some values from: gap separation distance setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: end gap separation penalty setting specification
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: clustering algorithm
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: multiple sequence alignment objective
subclass of: Restriction
  on property: has_specified_input
  some values from: gap extension penalty setting specification
subclass of: Restriction
  on property: realizes
  some values from: Restriction
    on property: concretizes
    some values from: pairwise sequence alignment algorithm
subclass of: Restriction
  on property: has_specified_input
  some values from: gap creation penalty setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: iteration strategy setting specification
definition source: WS Annotations Group, UGA
alternative term: multiple sequence alignment
editor note: Ready for OBI-WS : v1.0
definition: 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.
term editor: ITPPR

lower triangular matrix
type: Class
subclass of: matrix
definition: A matrix with equal number of rows and columns for which all the elements above the main diagonal have values equal to 0.
term editor: WS annotations Group, UGA
definition source: Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29

sequence alignment data set
type: Class
subclass of: data set
definition: A data set that is produced as the output of some sequence alignment process.
term editor: WS Annotations Group, UGA
definition source: WS Annotations Group, UGA

sequence alignment data format specification
type: Class
subclass of: data format specification
definition: A data format specification that specifies the data format for the outcome of sequence alignment (pairwise or multiple) process.
term editor: ITPPR
editor note: Ready for OBI-WS : v1.0
definition source: ITPPR

multiple sequence alignment data format specification
type: Class
subclass of: sequence alignment data format specification
subclass of: Restriction
  on property: is about
  some values from: multiple sequence alignment data set
definition source: WS Annotations Group, UGA
definition: 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
editor note: Ready for OBI-WS : v1.0
term editor: WS Annotations Group, UGA

order of sequences in alignment setting specification
type: Class
subclass of: software execution setting specification
alternative term: order of sequences in alignment
definition source: ClustalW Web service Documentation
term editor: WS Annotations Group, UGA
definition: 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
type: Class
subclass of: symbol
alternative term: job status
definition: 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
definition source: ClustalW Web service Documentation www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
term editor: WS Annotations Group, UGA

fast pairwise sequence alignment data transformation
type: Class
subclass of: pairwise sequence alignment data transformation
subclass of: Restriction
  on property: has_specified_input
  some values from: fast pairwise alignment scoring method setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: gap penalty setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: number of match regions setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: alignment word size setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: alignment window size setting specification
definition: 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.
editor note: are local, fast and slow pairwise alignments disjoint
term editor: ITPPR
definition source: ClustalW Documentation
editor note: Ready for OBI-WS : v1.0
alternative term: fast pairwise sequence alignment

filter sequence data objective
type: Class
subclass of: objective specification
definition source: ITPPR
term editor: ITPPR
definition: 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
type: Class
subclass of: retrieve web service execution result objective
editor note: Assign IDs
term editor: ITPPR
definition: 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.
definition source: SignalP Web service documentation

display multiple HSPs setting specification
type: Class
subclass of: software execution setting specification
term editor: ITPPR
definition source: FASTA Web service documentation
alternative term: display multiple HSPs
definition: 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
type: Class
subclass of: objective specification
term editor: ITPPR
definition: An objective specification that describes the goal of retrieving the supported output data formats for a particular web service execution.
definition source: ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa

base64 encoding specification
type: Class
subclass of: MIME type specification
definition: 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.
definition source: http://en.wikipedia.org/wiki/Base64
term editor: ITPPR

protein signature recognition algorithm
type: Class
subclass of: algorithm
definition source: EBI online courses : http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/what-are-protein-signatures
term editor: ITPPR
definition: An algorithm or a predictive model to predict the presence of a particular protein signature.
editor note: assign ids

retrieve web service execution result
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: retrieve web service execution result objective
definition source: ITPPR
alternative term: get result
term editor: ITPPR
definition: 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
type: Class
subclass of: data item
definition source: SignalP Web service documentation
editor note: ITPPR
definition: 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
type: Class
subclass of: quantitative confidence value
definition: A quantitative confidence value that acts as a threshold score to determine if the sequence pattern in consideration is a signal peptide or not.
definition source: SignalP Web service documentation
term editor: ITPPR

identify protein signature execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: protein sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: web service execution identifier
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: is about
      all values from: protein signature recognition algorithm
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: identify protein signature objective
definition: A web service execution that tries to locate occurrence of different known protein signatures like signal peptides in a protein sequence.
term editor: ITPPR
definition source: InterPro Documentation at EBI : ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/FAQs.html

software execution setting specification
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is_specified_input_of
  some values from: software execution
definition source: ITPPR
term editor: ITPPR
definition: 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.
alternative term: program setting parameter

signal peptides prediction outcome
type: Class
subclass of: data item
definition source: SignalP Web service documentation / ITPPR
definition: 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.
term editor: ITPPR

comma separated values data format specification
type: Class
subclass of: data format specification
definition source: http://en.wikipedia.org/wiki/Comma-separated_values
editor note: assign id
term editor: ITPPR
alternative term: CSV data format
definition: A data format specification that consists of any number of records and each record separated by a comma (',').

identify protein signature objective
type: Class
subclass of: objective specification
definition source: InterProScan Documentation at EBI
term editor: ITPPR
definition: An objective specification that describes the goal of identifying protein signatures in a protein sequence.

retrieve web service execution result objective
type: Class
subclass of: objective specification
editor note: assign id
definition source: ITPPR
term editor: ITPPR
definition: 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
type: Class
subclass of: predicted protein signatures data set
subclass of: Restriction
  on property: has part
  some values from: signal peptides prediction outcome
subclass of: Restriction
  on property: has part
  some values from: signal peptide prediction score
term editor: ITPPR
definition source: SignalP Web service documentation
definition: 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
type: Class
subclass of: web service execution identifier
alternative term: ITPPR
definition: A web service execution identifier that uniquely identifies a submitted a phylip web service execution.
editor note: Check how much it effect Suggestion..!! Obsolete it.!
definition source: ITPPR

construct phylogenetic trees objective
type: Class
subclass of: sequence analysis objective
definition source: http://en.wikipedia.org/wiki/Phylogenetic_tree#Unrooted_tree
term editor: ITPPR
definition: 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
type: Class
subclass of: algorithm
definition: An algorithm that is the method for construction of consensus tree.
term editor: ITPPR
definition source: ITPPR

phylogenetic tree
type: Class
subclass of: data set
subclass of: Restriction
  on property: has part
  some values from: protein sequence data
definition source: http://evolution.genetics.washington.edu/phylip/doc/neighbor.html
definition: 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.
term editor: ITPPR

evolution based amino acid substitution matrix
type: Class
subclass of: amino acid substitution matrix
subclass of: Restriction
  on property: is about
  some values from: amino acids
term editor: ITPPR
definition source: http://molecularevolution.org/resources/models/aa
definition: 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
type: Class
subclass of: sequence analysis objective
term editor: ITPPR
definition: A sequence analysis objective that aims to compute a protein distance matrix for a multiple sequence alignment using a suitable amino acid replacement model.
definition source: http://cmgm.stanford.edu/phylip/protdist.html#0

consensus tree
type: Class
subclass of: phylogenetic tree
term editor: ITPPR
definition source: http://evolution.genetics.washington.edu/phylip/doc/consense.html
definition: A phylogenetic tree that is a cladogram which summarizes agreement between two or more phylogenetic trees.

genetic code
type: Class
subclass of: data set
definition: 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).
term editor: ITPPR
definition source: http://en.wikipedia.org/wiki/Genetic_code

construct consensus tree execution
type: Class
subclass of: phylip execution
subclass of: Restriction
  on property: has_specified_input
  on class: phylogenetic tree
  min qualified cardinality: 2
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: algorithm identifier
    intersection of: Restriction
      on property: is about
      all values from: consensus tree construction algorithm
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: construct phylogenetic trees objective
definition: A phylip execution that constructs a consensus tree that summarizes the agreement between two or more phylogenetic trees.
term editor: ITPPR
definition source: http://evolution.genetics.washington.edu/phylip/doc/consense.html

transcript sequence data
type: Class
subclass of: RNA sequence data
definition: A RNA sequence data that is about the primary structure of RNA sequence produced by transcription.
term editor: ITPPR
definition source: ITPPR
alternative term: Predicted RNA/mRNA Sequence (introns spliced out).

minimum signalp D score setting specification
type: Class
subclass of: software execution setting specification
definition: 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).
term editor: ITPPR
definition source: ITPPR
alternative term: min sigp D score

minimum signalp sum score setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
definition source: ITPPR
term editor: ITPPR
alternative term: min sigp sum score

minimum signalp probability setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the minimum value of signal probability from SignalP-HMM.
definition source: ITPPR
term editor: ITPPR
alternative term: min sigp signal probability

any or all signalp setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies Union or intersection of advanced parameters.
definition source: ITPPR
term editor: ITPPR

find genes objective
type: Class
subclass of: objective specification
definition: An objective specification of retrieving genes based on different parameters (e.g., gene locus tag, taxonomy or signal peptide etc.).
term editor: ITPPR
definition source: ITPPR

find genes by taxonomy execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
definition: A web service execution that retrieves all genes of one or more species/organism(s).
definition source: ITPPR
term editor: ITPPR

gene locus tag
type: Class
subclass of: CRID symbol
subclass of: Restriction
  on property: denotes
  some values from: primary structure of DNA macromolecule
definition: A CRID symbol that is systematically applied to every gene in a genome within the context of sequencing projects.
alternative term: Gene ID
term editor: ITPPR
definition source: EMBL-EBI

RNA sequence data
type: Class
subclass of: sequence data
subclass of: Restriction
  on property: is about
  some values from: primary structure of RNA molecule
definition: A sequence data that is about the primary structure of RNA.
term editor: ITPPR
definition source: ITPPR

coding sequence data
type: Class
subclass of: DNA sequence data
definition: A sequence data that is about primary structure of coding sequence of DNA.
alternative term: Coding Sequence
term editor: ITPPR
definition source: ITPPR

protein sequence length
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: polypeptide
definition: A data item that represents length of predicted protein sequence.
term editor: ITPPR
definition source: ITPPR
alternative term: Protein Length.

find genes using signal peptide execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum signalp D score setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum signalp probability setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum signalp sum score setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: any or all signalp setting specification
definition: A web service execution that retrieves all genes that are predicted to encode a signal peptide.
definition source: ITPPR
term editor: ITPPR

genomic location of gene
type: Class
subclass of: data item
subclass of: Restriction
  on property: is about
  some values from: primary structure of DNA macromolecule
term editor: ITPPR
definition: 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.
definition source: CBIL-UPENN
example of usage: 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.
alternative term: location text

find genes by locus tag execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: has_specified_input
  some values from: gene locus tag
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
definition: A web service execution that retrieves genes using list of comma separated gene locus tag.
definition source: ITPPR
term editor: ITPPR

maximum isoelectric point setting secification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the upper bound for the protein isoelectric point.
term editor: ITPPR
definition source: ITPPR
alternative term: maximum isoelectric point

minimum number of predicted transmembrane domains setting specification
type: Class
subclass of: software execution setting specification
definition source: A software execution setting specification that specifies the lower bound on number of predicted transmembrane domains a protein may have.
definition source: ITPPR
term editor: ITPPR
alternative term: minimum number of predicted transmembrane domains

minimum isoelectric point setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the lower bound for the protein isoelectric point.
definition source: ITPPR
term editor: ITPPR
alternative term: minimum isoelectric point

epitope confidence setting specification
type: Class
subclass of: software execution setting specification
definition: 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.
definition source: ITPPR
term editor: ITPPR
example of usage: The epitope confidence can be specified as High, Medium or Low.
alternative term: epitope confidence

find genes by transmembrane domain execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum number of predicted transmembrane domains setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_input
  some values from: maximum number of predicted transmembrane domains setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
definition: A web service execution that retrieves all genes having number of predicted transmembrane domains in a range that user specify.
term editor: ITPPR
definition source: ITPPR
alternative term: find genes by transmembrane domain

find genes with epitopes execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_input
  some values from: epitope confidence setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
definition: 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.
term editor: ITPPR
definition source: ITPPR
alternative term: find genes with epitopes

find genes by molecular weight execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum molecular weight setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: maximum molecular weight setting specification
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
definition: A web service execution that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify.
term editor: ITPPR
definition source: ITPPR
alternative term: find genes by molecular weight

minimum molecular weight setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the minimum value for protein molecular weight.
definition source: ITPPR
term editor: ITPPR
alternative term: minimum molecular weight

maximum molecular weight setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the maximum value for protein molecular weight.
term editor: ITPPR
definition source: ITPPR
alternative term: maximum molecular weight

maximum number of predicted transmembrane domains setting specification
type: Class
subclass of: software execution setting specification
definition: A software execution setting specification that specifies the upper bound on number of predicted transmembrane domains a protein may have.
term editor: ITPPR
definition source: ITPPR
alternative term: maximum number of predicted transmembrane domains

find genes by isoelectric point execution
type: Class
subclass of: web service execution
subclass of: Restriction
  on property: has_specified_input
  some values from: minimum isoelectric point setting specification
subclass of: Restriction
  on property: has_specified_input
  some values from: maximum isoelectric point setting secification
subclass of: Restriction
  on property: has_specified_output
  some values from: gene locus tag
subclass of: Restriction
  on property: achieves_planned_objective
  some values from: find genes objective
subclass of: Restriction
  on property: has_specified_output
  some values from: transcript sequence data
subclass of: Restriction
  on property: has_specified_input
  some values from: Class
    intersection of: textual entity
    intersection of: Restriction
      on property: denotes
      some values from: organism
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence length
subclass of: Restriction
  on property: has_specified_output
  some values from: genomic location of gene
subclass of: Restriction
  on property: has_specified_output
  some values from: coding sequence data
subclass of: Restriction
  on property: has_specified_output
  some values from: protein sequence data
definition: A web service execution that retrieves all genes whose protein product has an isoelectric point in a range that user specify.
definition source: ITPPR
term editor: ITPPR
alternative term: find genes by isoelectric point

region
type: Class
subclass of: generically dependent continuant
alternative term: primary structure of sequence macromolecule
alternative term: sequence
definition: 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.
editor preferred term: region
imported from: so.owl

polypeptide
type: Class
subclass of: region
alternative term: polypeptide sequence
definition: A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
editor preferred term: polypeptide
imported from: so.owl

polymer_attribute
type: Class
subclass of: quality
imported from: http://purl.obolibrary.org/obo/so.owl
definition: An attribute to describe the kind of biological sequence.

example to be eventually removed
type: Thing
type: curation status specification
type: NamedIndividual

metadata complete
type: Thing
type: curation status specification
type: NamedIndividual
definition: 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
type: Thing
type: curation status specification
type: NamedIndividual
term editor: PERSON:Alan Ruttenberg
definition: term created to ease viewing/sort terms for development purpose, and will not be included in a release

ready for release
type: Thing
type: curation status specification
type: NamedIndividual
definition: 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
type: Thing
type: curation status specification
type: NamedIndividual
definition: Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.

uncurated
type: Thing
type: curation status specification
type: NamedIndividual
definition: Nothing done yet beyond assigning a unique class ID and proposing a preferred term.

pending final vetting
type: Thing
type: curation status specification
type: NamedIndividual
definition: 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
type: NamedIndividual
type: curation status specification
term editor: Alan Ruttenberg
definition: Terms with this status should eventually replaced with a term from another ontology.
definition source: group:OBI

requires discussion
type: NamedIndividual
type: curation status specification
definition: 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.
term editor: Alan Ruttenberg
definition source: group:OBI

PAM
type: NamedIndividual
type: evolution based amino acid substitution matrix

BLOSUM62
type: NamedIndividual
type: amino acid substitution matrix
has_dimension: 20

absolute
type: NamedIndividual
type: fast pairwise alignment scoring method setting specification

both
type: NamedIndividual
type: gene strand specifier

percent
type: NamedIndividual
type: fast pairwise alignment scoring method setting specification

BLASTp
type: NamedIndividual
type: BLAST algorithm
definition: A BLAST algorithm that searches/aligns a protein query sequence against a protein database at a protein level.

BLASTx
type: NamedIndividual
type: BLAST algorithm
definition: A BLAST algorithm that searches/aligns a nucleotide query sequence against a protein database at a protein level.

BLASTn
type: NamedIndividual
type: BLAST algorithm
definition: A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level.

FASTA
type: NamedIndividual
type: sequence data format specification

aligned
type: NamedIndividual
type: order of sequences in alignment setting specification

Poisson
type: NamedIndividual
type: pairwise alignment statistical model setting specification

bottom
type: NamedIndividual
type: gene strand specifier

input
type: NamedIndividual
type: order of sequences in alignment setting specification

kap
type: NamedIndividual
type: pairwise alignment statistical model setting specification

sump
type: NamedIndividual
type: pairwise alignment statistical model setting specification

high
type: NamedIndividual
type: pairwise alignment sensitivity setting specification

seg+xnu
type: NamedIndividual
type: low complexity sequence filter algorithm identifier

tBLASTn
type: NamedIndividual
type: BLAST algorithm
definition: A BLAST algorithm that searches/aligns a protein query sequence against a nucleotide database at a protein level.

top
type: NamedIndividual
type: gene strand specifier

low
type: NamedIndividual
type: pairwise alignment sensitivity setting specification

seg
type: NamedIndividual
type: low complexity sequence filter algorithm identifier

xnu
type: NamedIndividual
type: low complexity sequence filter algorithm identifier

medium
type: NamedIndividual
type: pairwise alignment sensitivity setting specification

tBLASTx
type: NamedIndividual
type: BLAST algorithm
definition: A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a protein level.

normal
type: NamedIndividual
type: pairwise alignment sensitivity setting specification