Release v1.1
This file is based on checkout of our SVN repository revision $Revision: 61 $
2012-12-18
en
Akshay Choche
Alok Dhamanaskar
An ontology for the annotation of bioinformatics web services.
An ontology that extends the Ontology for Biomedical Investigations (OBI) to build an Ontology that supports consistent annotation of Bioinformatics Web services.
Chaitanya Guttula
Chris Stoeckert
Jessie Kissinger
Jie Zheng
John Miller
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
definition
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
editor note
has curation status
OBI_0000281
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
has curation status
imported from
For external terms/classes, the ontology from which the term was imported
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Alan Ruttenberg
PERSON:Melanie Courtot
imported from
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
curator note
An administrative note of use for a curator but of no use for a user
PERSON:Alan Ruttenberg
curator note
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
PERSON:Daniel Schober
term editor
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
alternative term
editor preferred term
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
editor preferred term
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
PERSON:Daniel Schober
example
is part of
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
part of
part_of
has part
has_part
inheres in
inheres_in
is bearer of
bearer of
bearer_of
is realized by
realized by
realized_by
realizes
participates in
participates_in
has participant
has_participant
is concretization of
concretization of
concretization_of
concretizes
s depends on
s_depends_on
is located in
located in
located_in
is about
7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive.
We will try to build it back up by elaborating the various subproperties that are more precisely defined.
Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
This document is about information artifacts and their representations
is_about is a (currently) primitive relation that relates an information artifact to an entity.
person:Alan Ruttenberg
denotes
2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.
g denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named.
Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan
denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically
person:Alan Ruttenberg
has_specified_input
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
is_specified_input_of
PERSON:Bjoern Peters
is_specified_input_of
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
Alan Ruttenberg
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_specified_output
PERSON: Bjoern Peters
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
PERSON: Alan Ruttenberg
is_specified_output_of
PERSON:Bjoern Peters
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
BP, AR, PPPB branch
PPPB branch derived
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
achieves_planned_objective
modified according to email thread from 1/23/09 in accordince with DT and PPPB branch
is_encoded_in
SWO proposed relation, link data with data format specification, or software with program language
is_encoded_of
is_executed_in
propose to deprecate
algorithm/software is_executed_in information process
is_executed_of
propose to deprecate
has_dimension
has_description
has_value
entity
entity
continuant
An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
a heart
a person
a symphony orchestra
continuant
endurant
the color of a tomato
the disposition of blood to coagulate
the lawn and atmosphere in front of our building
the mass of a cloud
occurrent
An entity that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
a surgical operation as processual context for a nosocomical infection
occurrent
perdurant
the life of an organism
the most interesting part of Van Gogh's life
the spatiotemporal context occupied by a process of cellular meiosis
the spatiotemporal region occupied by the development of a cancer tumor
independent continuant
A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything.
a chair
a heart
a leg
a person
a symphony orchestra
an organism
independent continuant
substantial entity
the bottom right portion of a human torso
the lawn and atmosphere in front of our building
dependent continuant
A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities.
dependent continuant
process
A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
process
the life of an organism
the process of cell-division
the process of sleeping
realizable entity
A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
realizable entity
the disposition of blood to coagulate
the disposition of metal to conduct electricity
the function of the reproductive organs
the role of being a doctor
quality
A specifically dependent continuant that is exhibited if it inheres in an entity or entities at all (a categorical property).
quality
the ambient temperature of air
the circumference of a waist
the color of a tomato
the mass of a piece of gold
the shape of a nose
the weight of a chimpanzee
specifically dependent continuant
A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
mode
property
specifically dependent continuant
the color of a tomato
the disposition of fish to decay
the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
the liquidity of blood
the mass of a cloud
the role of being a doctor
the smell of mozzarella
trope
role
A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts.
role
the role of a biological grandfather as legal guardian in the context of a system of laws
the role of a chemical compound in an experiment
the role of a patient relative as defined by a hospital administrative form
the role of a person as a surgeon
the role of a student in a university
the role of a woman as a legal mother in the context of system of laws
the role of ingested matter in digestion
generically dependent continuant
A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.
a certain PDF file that exists in different and in several hard drives
generically dependent continuant
material entity
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
Examples: collection of random bacteria, a chair, dorsal surface of the body
Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology.
material entity
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acids
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
molecular entity
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
ribonucleic acids
Naturally occurring polyribonucleotides.
ribonucleic acids
amino acids
Carboxylic acids containing one or more amino groups.
amino acids
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule
polymer
objective specification
2009-03-16: original definition when imported from OBI read: "objective is an
non realizable information entity which can serve as that proper part
of a plan towards which the realization of the plan is directed."
Answers the question, why did you do this experiment?
OBI Plan and Planned Process/Roles Branch
OBI_0000217
PERSON: Alan Ruttenberg
PERSON: Barry Smith
PERSON: Bjoern Peters
PERSON: Jennifer Fostel
a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved.
objective specification
purpose of a study; support of hypothesis, discovery of new information
action specification
Alan Ruttenberg
OBI Plan and Planned Process branch
Pour the contents of flask 1 into flask 2
a directive information entity that describes an action the bearer will take
datum label
9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum.
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
GROUP: IAO
datum label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
software
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Chris Stoeckert
PERSON: Melanie Courtot
Software is a plan specification composed of a series of instructions that can be
interpreted by or directly executed by a processing unit.
see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178
software
data item
2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
Data items include counts of things, analyte concentrations, and statistical summaries.
JAR: datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
JAR: A data item is an approximately justified approximately true approximate belief
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
data
data item
symbol
20091104, MC: this needs work and will most probably change
PERSON: Jonathan Rees
a smallish, word-like datum...
symbol
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
OBI_0000142
PERSON: Chris Stoeckert
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information content entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
directive information entity
2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be
concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
algorithm
A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
OBI_0000270
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
curation status specification
data format specification
2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes
information. Example: The ISO document specifying what encompasses an
XML document; The instructions in a XSD file"
A data format specification is the information content borne by the document published defining the specification.
Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
OBI branch derived
OBI_0000187
PERSON: Alan Ruttenberg
PlanAndPlannedProcess Branch
data format specification
data set
2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type
A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.
Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).
OBI_0000042
data set
group:OBI
person:Allyson Lister
person:Chris Stoeckert
data about an ontology part
Person:Alan Ruttenberg
data about an ontology part is a data item about a part of an ontology, for example a term
plan specification
2/3/2009 Comment from OBI review.
Action specification not well enough specified.
Conditional specification not well enough specified.
Question whether all plan specifications have objective specifications.
Request that IAO either clarify these or change definitions not to use them
2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term.
Alan Ruttenberg
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI Plan and Planned Process branch
OBI_0000344
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications.
plan specification
measurement datum
2/2/2009 is_specified_output of some assay?
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
OBI_0000305
group:OBI
measurement datum
person:Chris Stoeckert
textual entity
A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
PERSON: Lawrence Hunter
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
text
textual entity
document
A collection of information content entities intended to be understood together as a whole
A journal article, patent application, laboratory notebook, or a book
PERSON: Lawrence Hunter
document
email address
Alan Ruttenberg 1/3/2012 - Provisional id, see issue at http://code.google.com/p/information-artifact-ontology/issues/detail?id=130&thanks=130&ts=1325636583
Person:Alan Ruttenberg
Person:Chris Stoeckart
email address
CRID symbol
A symbol that is part_of a CRID and that is sufficient to look up a record from the CRID's registry.
IAO call, 20101124: 12345 is not a CRID symbol. To be a CRID symbol you need to have some information about the registry within which the CRID is recorded.
Original proposal from Bjoern, discussions at IAO calls
PERSON: Alan Ruttenberg
PERSON: Bill Hogan
PERSON: Bjoern Peters
PERSON: Melanie Courtot
PMID:12345, 12345 in a database column which has header "pubmedID"
Viruses
Viruses
Teleostomi
Teleostomi
Euteleostomi
Euteleostomi
Bacteria
Bacteria
Homo/Pan/Gorilla group
Homo/Pan/Gorilla group
Archaea
Archaea
Eukaryota
Eukaryota
Euarchontoglires
Euarchontoglires
Simiiformes
Simiiformes
Hominoidea
Hominoidea
Tetrapoda
Tetrapoda
Amniota
Amniota
Theria
Theria
Fungi/Metazoa group
Fungi/Metazoa group
Metazoa
Metazoa
Bilateria
Bilateria
Coelomata
Coelomata
Deuterostomia
Deuterostomia
Haplorrhini
Haplorrhini
Mammalia
Mammalia
Eumetazoa
Eumetazoa
Chordata
Chordata
Vertebrata
Vertebrata
Gnathostomata
Gnathostomata
Sarcopterygii
Sarcopterygii
Craniata
Craniata
Eutheria
Eutheria
Primates
Primates
Catarrhini
Catarrhini
Hominidae
Hominidae
Homo
Homo
Homo sapiens
human being
Homo sapiens
planned process
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
6/11/9: Edited at workshop. Used to include: is initiated by an agent
Bjoern Peters
Injecting mice with a vaccine in order to test its efficacy
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
branch derived
A processual entity that realizes a plan which is the concretization of a plan specification.
This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
planned process
quantitative confidence value
group:OBI
A data item which is used to indicate the degree of uncertainty about a measurement.
person:Chris Stoeckert
quantitative confidence value
organization
GROUP: OBI
PERSON: Alan Ruttenberg
PERSON: Bjoern Peters
PERSON: Philippe Rocca-Serra
PERSON: Susanna Sansone
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
organization
primary structure of DNA macromolecule
BP et al
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
primary structure of DNA macromolecule
primary structure of RNA molecule
Person:Bjoern Peters
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
primary structure of RNA molecule
record of missing knowledge
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
Bjoern Peters
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
service consumer role
A biologist who uses a sequencing services fulfills the role of a service consumer
OBI
Person:Helen Parkinson
a role which inheres in a person who uses a service
service consumer role
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
PERSON:Helen Parkinson
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
sequence data
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
GROUP: OBI
Person:Chris Stoeckert
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
sequence data
service
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
Carlo; Matt
OBI workshop San Diego 2011
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
service
DNA sequence data
8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there.
A sequence data item that is about the primary structure of DNA
DNA sequence data
OBI call; Bjoern Peters
OBI call; Melanie Courtout
The part of a FASTA file that contains the letters ACTGGGAA
organism
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
GROUP: OBI Biomaterial Branch
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
WEB: http://en.wikipedia.org/wiki/Organism
animal
fungus
organism
plant
virus
data transformation
Philippe Rocca-Serra
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
A data transformation is a process which produces output data from input data
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
data analysis
data processing
data transformation
sequence analysis objective
James Malone
PERSON: James Malone
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
sequence analysis objective
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
James Malone
PERSON: James Malone
data transformation objective
normalize objective
digital document name
ITPPR
A textual entity that refers to a digital document derived from a computer system.
ITPPR
file name
file extension
A textual entity that is the suffix for a file name.
EDAM: file extension
WS annotations Group, UGA
metadata of data format specification
A textual entity that gives the details of the different supported data formats and associated file extension and other metadata.
WS annotations Group, UGA
ClustalW Web service Documentation
MIME type specification
A data format specification that is used to specify the content type over the Web. (MIME is an acronym for Multipurpose Internet Mail Extension)
Ready for OBI-WS : v1.0
Wikipedia: en.wikipedia.org/wiki/MIME
WS Annotations Group, UGA
clustering algorithm
WS Annotations Group, UGA
Ready for OBI-WS : v1.0
An algorithm that assigns set of observations/data into subsets (called clusters) so that observations/data in the same cluster are similar in some sense.
Wikipedia: en.wikipedia.org/wiki/Nearest_neighbor_search
sequence similarity identification objective
A sequence analysis objective that describes the aim to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
ITPPR
EDAM: alignment
Ready for OBI-WS : v1.0
pairwise sequence alignment algorithm
An algorithm that attempts to align two molecular sequences (nucleic acid or protein sequences).
WS Annotations Group, UGA
WS Annotations Group, UGA
Ready for OBI-WS : v1.0
multiple sequence alignment algorithm
An algorithm that is used to obtain multiple sequence alignments between nucleotide or protein sequences.
Ready for OBI-WS : v1.0
ITPPR
ITPPR
gap separation distance setting specification
ClustalW Web service Documentation and WS annotations Group, UGA
A software execution setting specification that specifies the distance between two consecutive gaps when aligning two sequences, within which introducing a new gap is penalized in addition to gap creation penalty.
WS Annotations Group, UGA
gap separation distance
end gap separation penalty setting specification
End Gap Separation: Treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by GAP SEPARATION DISTANCE above). If you turn this off, end gaps will be ignored for this purpose. This is useful when you wish to align fragments where the end gaps are not biologically meaningful.
WS Annotations Group, UGA
end gap separation penalty
ClustalW Web service Documentation and WS annotations Group, UGA
A software execution setting specification that states whether or not to apply the gap extension penalty when scoring terminal gaps using a Boolean value.
configuration parameter which is a Boolean value, that states whether or not to apply the gap extension penalty when scoring terminal gaps.
number of iterations setting specification
number of iterations
ClustalW Web service Documentation
WS Annotations Group, UGA
A software execution setting specification that specifies the maximum number of iterations to perform.
iteration strategy setting specification
ClustalW Web service Documentation
iteration strategy
WS Annotations Group, UGA
A software execution setting specification that specifies the multiple alignment improvement iteration type. For clustalW, It can take values: none, tree(Iteration at each step of alignment process) or alignment(Iteration only on final alignment).
algorithm identifier
ITPPR
ITPPR
A symbol that specifies a particular algorithm to be implemented in a tool or software.
multiple sequence alignment guide tree
A data item which is a tree that represents the relationship between sequences and is used to build the multiple sequence alignment. For the first iteration of multiple sequence alignment process the guide tree is constructed by a clustering method while for the subsequent iterations it is constructed from the previous iteration.
Wikipedia : http://en.wikipedia.org/wiki/Multiple_sequence_alignment
ITPPR
retrieve alignment result objective
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
A retrieve web service execution result objective that describes the goal of retrieving the sequence alignment result.
Ready for OBI-WS : v1.0
WS Annotations Group, UGA
web service execution identifier
Unique identifier for Web Service job
job id
A CRID symbol used to uniquely identify a submitted web service execution.
ITPPR
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
multiple sequence alignment data set
WS Annotations Group, UGA
A sequence alignment data set that is produced as the output of a multiple sequence alignment process.
WS Annotations Group, UGA
web service execution title
job title
ClustalW Web service Documentation
A textual entity that is the name of a web service job submitted.
ITPPR
filter sequence data
A web service execution that filters sequence data depending on their similarity score to a specified sequence and expectation value.
ITPPR
ITPPR
gap creation penalty setting specification
A gap penalty setting specification that specifies the penalty for introducing a new gap when producing an alignment.
gap creation penalty
EDAM: gap creation penalty
WS Annotations Group, UGA
DNA substitution matrix
A scoring matrix that is used for scoring alignment of nucleotide sequences.
WS annotations Group, UGA
WS annotations Group, UGA
protein distance matrix
A Matrix that stores the evolutionary distance between each pair of protein sequences, with each species starting on a new line with the species name, followed by the distances to the species in order.
WS annotations Group, UGA
http://cmgm.stanford.edu/phylip/protdist.html
compute protein evolution distance execution
A phylip execution that computes a protein evolution distance matrix using a amino acid replacement model.
ITPPR
http://cmgm.stanford.edu/phylip/protdist.html#0
gap extension penalty setting specification
Ready for OBI-WS : v1.0
gap extension penalty
WS Annotations Group, UGA
EDAM: gap extension penalty
A gap penalty setting specification that specifies the penalty for extending a gap when aligning sequences.
construct phylip neighbor tree execution
A phylip execution that constructs an unrooted phylogenetic tree from a protein distance matrix by successive clustering using either Neighbor joining or UPGMA method of clustering.
ITPPR
http://evolution.genetics.washington.edu/phylip/doc/neighbor.html
phylip execution
A web service execution that involves invocation of different programs for inferring phylogenetic relationships between groups of organisms.
http://en.wikipedia.org/wiki/Phylogenetics, http://www.phylip.com/
ITPPR
get web service execution status
ITPPR
A web service execution that returns the status (e.g. Finished, Running) of a web service execution, depending upon web service execution identifier. .
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
get job status
clustalW execution
ClustalW Web service Documentation
A web service execution that performs multiple sequence alignment.
ITPPR
get supported output data format
A web service execution that retrieves all the supported output data format for a particular execution.
ITPPR
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
get result types
retrieve alignment result execution
ClustalW Web service Documentation
WS annotations Group, UGA
A retrieve web service execution result that would fetch the result of alignment analysis given its unique execution identifier.
web service
A service that exposes an arbitrary set of operations which can be accessed through a programmatic interface to a web server maintained by the service provider.
Wikipedia: http://en.wikipedia.org/wiki/Web_service
ITPPR
amino acid substitution matrix
There are two options for the protein weight matrix: BLOSUM and PAM. The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are. Different matrices work differently at each evolutionary distance.
WS annotations Group, UGA
http://en.wikipedia.org/wiki/Substitution_matrix
A scoring matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time.
software execution
ITPPR
ITPPR
operation
A planned process that realizes the concretization of a software.
scoring matrix
A lower triangular matrix where each cell represents a score to be assigned to a specific type of pairing of nucleotide or amino acid sequences generally used in sequence alignment.
WS annotations Group, UGA
WS annotations Group, UGA
gap penalty setting specification
WS Annotations Group, UGA
EDAM: gap Penalty
gap penalty
A software execution setting specification that specifies the penalty value for each gap introduced when aligning sequences (accounts for both gap creation and gap extension penalties). It has little affect on the speed or sensitivity except for extreme values.
invoke software execution over network objective
ITPPR
ITPPR
An objective specification that a web service execution accomplishes.
Ready for OBI-WS : v1.0
number of match regions setting specification
number of matched regions
A software execution setting specification that specifies the number of k-tuple matches on each diagonal used to create pairwise alignment. Decrease for speed; increase for sensitivity.
ClustalW Web service Documentation
WS Annotations Group, UGA
fast pairwise alignment scoring method setting specification
ClustalW Web service Documentation
A software execution setting specification that specifies the output type for fast pairwise alignment score (can be either percent or absolute).
WS Annotations Group, UGA
fast pairwise alignment scoring method
alignment window size setting specification
WS Annotations Group, UGA
alignment window size
ClustalW Web service Documentation
A software execution setting specification that specifies the number of diagonals around each of the 'best' diagonals that will be used for joining word matches. Decrease for speed; increase for sensitivity.
alignment word size setting specification
ClustalW Web service Documentation
WS Annotations Group, UGA
alignment word size
A software execution setting specification that specifies the alignment word size used to find matches between the sequences. A higher value increases the speed of the alignment but decreases the sensitivity.
multiple sequence alignment objective
A sequence similarity identification objective that aims to align multiple sequences at a time to determine the equivalence between them.
Ready for OBI-WS : v1.0
ITPPR
EDAM: alignment & ITPPR
pairwise sequence alignment objective
A sequence similarity identification objective that aims to align two sequences at a time to determine the equivalence between them.
WS Annotations Group, UGA
WS Annotations Group, UGA
Ready for OBI-WS : v1.0
number of top combinations setting specification
A software execution setting specification that specifies the number of HSPs to be reported, such that any given HSP is allowed to be a member of just one set. Values: a numerical value or 'All'
ITPPR
WU-Blast Web service documentation
number of top combinations
pairwise alignment sensitivity setting specification
A software execution setting specification that specifies the sensitivity level of the search performed, it can take following values (very low, low,normal, medium, high).
ITPPR
WU-Blast Web service documentation
pairwise alignment sensitivity
pairwise alignment statistical model setting specification
A software execution setting specification that specifies a statistical model to use for scoring alignments (pairwise). Can take values from (sum p, Poisson, kap).
WU-BLAST Web service documentation
ITPPR
pairwise alignment statistical model
pairwise alignment data format specification
A data format specification that specifies the format for the data produced as a result of pairwise sequence alignment. e.g. BLASTXML
Ready for OBI-WS : v1.0
WUBlast Web service documentation
ITPPR
low complexity sequence filter algorithm identifier
A sequence filter algorithm identifier that specifies an algorithm to pre-process the query sequence, such that the low complexity regions in the sequence are filtered out before sequence alignment as low complexity regions tend to give a false estimate of the similarity score.
http://www.ebi.ac.uk/Tools/sss/wublast/help/index-protein.html#filter
ITPPR
sequence filter algorithm identifier
A data item which specifies a sequence filter that pre-processes the query sequence before alignment to remove the undesired portions of it.
WU-BLAST Web service documentation
ITPPR
inclusion of filtered sequences setting specification
A software execution setting specification that specifies whether or not to show in the output file the query sequence used for the search, post filtering. Filtering here refers to masking of low complexity regions.
WU-BLAST Web service documentation
inclusion of filtered sequences
ITPPR
maximum match score setting specification
A software execution setting specification that specifies the maximum number of match scores displayed in the output.
ITPPR
maximum match score
WU-BLAST Web service documentation
sequence range setting specification
A software execution setting specification that defines the range of query sequence to use for search.
ITPPR
sequence range
NCBI BLAST Web service documentation
maximum number of matched alignments setting specification
A software execution setting specification that specifies the maximum number of alignments displayed in the output.
WU-BLAST Web service documentation
maximum number of matched alignment
ITPPR
gene strand specifier
A textual entity that specifies the DNA strand, upper, lower or both of a specific gene to be considered in alignment.
ITPPR
WU-BLAST Web service documentation
drop-off score setting specification
A software execution setting specification that determines the minimum allowable score for a sequence to be matched after which the algorithm gives up on aligning that sequence.
ITPPR
drop-off score
NCBI BLAST Web service documentation
sequence database for similarity search
A data set that is stored on a computer and used for molecular sequence similarity search.
WEBSITE:http://en.wikipedia.org/wiki/Sequence_database
ITPPR
pairwise alignment hits ordering setting specification
A software execution setting specification that specifies the ordering criteria that is used to order the sequences (before displaying) that matched the search criteria.
For example : The results could be ordered by the expectation value of sequences or using some other quantity like their score.
WU-BLAST Web service documentation
pairwise alignment hits ordering
ITPPR
protein sequence data
OBI / ITPPR
A sequence data that is about sequence of amino acids which are linked by peptide bonds.
ITPPR
data format specification identifier
A symbol used to identify (uniquely for a particular web service) the output type.
result type identifier
WS annotations Group, UGA
WS annotations Group, UGA
sequence similarity expectation value
A quantitative confidence value which determines a threshold value such that only alignments scoring more than this value are considered.
expectation value
WUBlast Web service documentation
ITPPR
retrieve signal peptide result
ITPPR
SignalP Web service documentation
A retrieve web service execution result that retrieves the outcome of a signal peptide prediction process given a unique web service execution identifier.
BLAST execution
A web service execution that performs local pairwise sequence alignment to search a database for similar sequences.
ITPPR
ITPPR
It is getting inferred as a Sequence alignment data Transformation is that what we want
signal peptide prediction algorithm
SignalP Web service documentation
A protein signature prediction method that serves as a prediction model to predict the location of signal peptides in a protein sequence.
ITPPR
predicted protein signatures data set
ITPPR
InterProScan Documentation
A data set that is as an outcome of protein signature prediction process.
BLAST algorithm
BLAST (Basic Local Alignment Search Tool), a pairwise sequence alignment algorithm is a heuristic search algorithm for comparing primary biological sequence information, such as the amino-acid or nucleotides sequences with a database of sequences, and identify sequences that resemble the query sequence above a certain threshold.
Wikipedia: BLAST
Ready for OBI-WS : v1.0
ITPPR
pairwise sequence alignment data transformation
A data transformation process that attempts to align two molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
Ready for OBI-WS : v1.0
EDAM: alignment & WS Annotations Group, UGA
ITPPR
pairwise sequence alignment
local pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that attempts to align two molecular sequences considering only parts of the sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
local pairwise sequence alignment
ITPPR
Ready for OBI-WS : v1.0
EDAM: alignment & WS Annotations Group, UGA
global multiple sequence alignment data transformation
A multiple sequence alignment data transformation that attempts to align the sequences considering their entire length.
WS Annotations Group, UGA
global multiple sequence alignment
Ready for OBI-WS : v1.0
ITPPR
check web service execution status objective
An objective specification that describes the goal of fetching the status of a web service execution.
Ready for OBI-WS : v1.0
ITPPR
check job status objective
record of missing annotation
A record of missing knowledge that describes terms in the document that are not present in the ontology.
unannotated term
WS Annotations Group, UGA
ITPPR
match mismatch scores setting specification
A software execution setting specification that specifies the scores for a match and miss-match, to be used when searching for similar nucleotide sequences.
NCBI BLAST Web service documentation
ITPPR
match mismatch scores
BLAST analysis data transformation
A local pairwise sequence alignment data transformation that performs pairwise sequence alignment to search sequence databases for similar sequences.
BLAST analysis
WS Annotations Group, UGA
Documentation for BLAST at NCBI
Ready for OBI-WS : v1.0
sequence identifier
A CRID symbol that serves as an identifier for a molecular sequence or for an entry from a molecular sequence database.
EDAM: sequence identifier
ITPPR
gaps alignment setting specification
A software execution setting specification which specifies whether the gapped areas in query sequence should be aligned in the process of sequence alignment or not using a Boolean value.
ITPPR
NCBIBlast Web service documentation
gaps alignment
matrix
WS annotations Group, UGA
Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29
A data set that is made up of a rectangular array of elements (or entries) set out by rows and columns.
fetch sequences execution
A web service execution that retrieves the sequence given the sequence identifier and the sequence database that has the sequence.
ITPPR
ITPPR
predict signal peptides
An identify protein signature execution that attempts to predict the presence and location of signal peptide cleavage sites in a protein sequence.
SignalP Web service documentation
ITPPR
predict signal peptide cleavage sites objective
An identify protein signature objective that describes the goal of predicting the presence and location of signal peptide cleavage sites in an amino acid sequence.
ITPPR
Ready for OBI-WS : v1.0
SignalP Web service documentation
web service execution
A software execution that is provided by the web service, and involves invoking software execution over network.
ITPPR
ITPPR
web service operation
sequence data format specification
A data format specification for molecular sequence feature information.
EDAM
sequence data format
ITPPR
Ready for OBI-WS : v1.0
fetch sequences objective
An objective specification of retrieving a sequence from a sequence database given the sequence identifier and the database that has the sequence.
retrieve sequences objective
ITPPR
Ready for OBI-WS : v1.0
ITPPR
display histograms setting specification
A software execution setting specification that is used to specify whether histogram is returned with the result of FASTA search using true or false Boolean value.
The histogram gives a qualitative view of how well the statistical theory fits the similarity scores calculated by the program.
display histograms
FASTA Web service documentation
slow pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that produces accurate alignments are carried out by using a dynamic programming method (Myers and Miller) to align every pair of sequences.
Ready for OBI-WS : v1.0
ClustalW Documentation
ITPPR
slow pairwise sequence alignment
multiple sequence alignment data transformation
WS Annotations Group, UGA
multiple sequence alignment
Ready for OBI-WS : v1.0
A data transformation that attempts to align multiple (more than two) molecular sequences in order to study the equivalence between sites of molecular sequences including nucleic acid and protein sequence.
ITPPR
lower triangular matrix
A matrix with equal number of rows and columns for which all the elements above the main diagonal have values equal to 0.
WS annotations Group, UGA
Wikipedia: http://en.wikipedia.org/wiki/Matrix_%28mathematics%29
sequence alignment data set
A data set that is produced as the output of some sequence alignment process.
WS Annotations Group, UGA
WS Annotations Group, UGA
sequence alignment data format specification
A data format specification that specifies the data format for the outcome of sequence alignment (pairwise or multiple) process.
ITPPR
Ready for OBI-WS : v1.0
ITPPR
multiple sequence alignment data format specification
WS Annotations Group, UGA
A data format specification that specifies the format for the data produced as a result of multiple sequence alignment. e.g. FASTA, PHYLIP, ALN W/Numbers
Ready for OBI-WS : v1.0
WS Annotations Group, UGA
order of sequences in alignment setting specification
order of sequences in alignment
ClustalW Web service Documentation
WS Annotations Group, UGA
A software execution setting specification that designates the order in which sequences appear in a final alignment. If ALIGNED option is chosen, the output order will be the order in which the sequences were aligned (from the guide tree/dendrogram). If INPUT option is chosen, the output will be in the same order as the input sequences.
web service execution status
job status
A symbol that is used to specify the status of a web service execution. It usually takes one of following values - DONE, ERROR, NOT_FOUND,PENDING, RUNNING
ClustalW Web service Documentation www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
WS Annotations Group, UGA
fast pairwise sequence alignment data transformation
A pairwise sequence alignment data transformation that produces Fast/Approximate alignments using the method of Wilbur and Lipman (1983) and may be more suitable for sequences longer than 1000 residues.
are local, fast and slow pairwise alignments disjoint
ITPPR
ClustalW Documentation
Ready for OBI-WS : v1.0
fast pairwise sequence alignment
filter sequence data objective
ITPPR
ITPPR
An objective specification that describes the goal of filtering sequence data depending on their similarity score to a specified sequence and expectation value.
retrieve signal peptide result objective
Assign IDs
ITPPR
A retrieve web service execution result objective that describes the goal of retrieving the result of an operation to predict the presence and location of signal peptide cleavage sites in amino acid sequences.
SignalP Web service documentation
display multiple HSPs setting specification
ITPPR
FASTA Web service documentation
display multiple HSPs
A software execution setting specification that specifies whether multiple high scoring alignments have to be displayed or not in the result using true or false Boolean value.
retrieve supported output data format objective
ITPPR
An objective specification that describes the goal of retrieving the supported output data formats for a particular web service execution.
ClustalW Web service Documentation : www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soapa
base64 encoding specification
A MIME type specification which represents an encoding scheme that represent binary data in an ASCII string format by translating it into a radix-64 representation.
http://en.wikipedia.org/wiki/Base64
ITPPR
protein signature recognition algorithm
EBI online courses : http://www.ebi.ac.uk/training/online/course/introduction-protein-classification-ebi/what-are-protein-signatures
ITPPR
An algorithm or a predictive model to predict the presence of a particular protein signature.
assign ids
retrieve web service execution result
ITPPR
get result
ITPPR
A web service execution that fetches the outcome of some previously executed web service operation (execution) given an execution identifier that is unique for that particular web service.
signal peptide prediction score
SignalP Web service documentation
ITPPR
A data item which is a score assigned for a signal peptide region predicted by a signal peptide prediction algorithm.
signal peptide prediction threshold value
A quantitative confidence value that acts as a threshold score to determine if the sequence pattern in consideration is a signal peptide or not.
SignalP Web service documentation
ITPPR
identify protein signature execution
A web service execution that tries to locate occurrence of different known protein signatures like signal peptides in a protein sequence.
ITPPR
InterPro Documentation at EBI : ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/FAQs.html
software execution setting specification
ITPPR
ITPPR
An information content entity which is an input setting parameter (usually optional) to some software execution that controls the way in which output is generated or displayed or which algorithm need to be executed.
program setting parameter
signal peptides prediction outcome
SignalP Web service documentation / ITPPR
A data item which is the outcome of predict signal peptide cleavage sites execution that specifies if a signal peptide chain is found or not.
ITPPR
comma separated values data format specification
http://en.wikipedia.org/wiki/Comma-separated_values
assign id
ITPPR
CSV data format
A data format specification that consists of any number of records and each record separated by a comma (',').
identify protein signature objective
InterProScan Documentation at EBI
ITPPR
An objective specification that describes the goal of identifying protein signatures in a protein sequence.
retrieve web service execution result objective
assign id
ITPPR
ITPPR
An objective specification that describes the goal of retrieving the outcome of some previously executed web service execution.
predicted signal peptide cleavage sites data set
ITPPR
SignalP Web service documentation
A predicted signal peptide cleavage sites data set that includes the outcome and all the meta data of signal peptide cleavage sites prediction process.
phylip execution identifier
ITPPR
A web service execution identifier that uniquely identifies a submitted a phylip web service execution.
Check how much it effect Suggestion..!!
Obsolete it.!
ITPPR
construct phylogenetic trees objective
http://en.wikipedia.org/wiki/Phylogenetic_tree#Unrooted_tree
ITPPR
A sequence analysis objective that describes the goal of constructing a phylogenetic tree that shows inferred evolutionary relationships between protein sequences.
consensus tree construction algorithm
An algorithm that is the method for construction of consensus tree.
ITPPR
ITPPR
phylogenetic tree
http://evolution.genetics.washington.edu/phylip/doc/neighbor.html
A data set which is a tree that represents evolutionary relationships between species, where the length of branches of the tree can signify evolutionary distance.
ITPPR
evolution based amino acid substitution matrix
ITPPR
http://molecularevolution.org/resources/models/aa
An amino acid substitution matrix that describes the probability at which one amino acid in a protein sequence changes to other amino acid over time calculated using an empirical model for protein evolution.
compute protein evolution distance objective
ITPPR
A sequence analysis objective that aims to compute a protein distance matrix for a multiple sequence alignment using a suitable amino acid replacement model.
http://cmgm.stanford.edu/phylip/protdist.html#0
consensus tree
ITPPR
http://evolution.genetics.washington.edu/phylip/doc/consense.html
A phylogenetic tree that is a cladogram which summarizes agreement between two or more phylogenetic trees.
genetic code
A data set that is a set of rules by which information encoded in genetic material (DNA or mRNA sequences) is translated into proteins (amino acid sequences).
ITPPR
http://en.wikipedia.org/wiki/Genetic_code
construct consensus tree execution
2
A phylip execution that constructs a consensus tree that summarizes the agreement between two or more phylogenetic trees.
ITPPR
http://evolution.genetics.washington.edu/phylip/doc/consense.html
transcript sequence data
A RNA sequence data that is about the primary structure of RNA sequence produced by transcription.
ITPPR
ITPPR
Predicted RNA/mRNA Sequence (introns spliced out).
minimum signalp D score setting specification
A software execution setting specification that specifies the minimum value of D-score which is the average of the S-mean and Y-max score from SignalP-NN (neural network).
ITPPR
ITPPR
min sigp D score
minimum signalp sum score setting specification
A software execution setting specification that specifies the minimum value of signalP summary conclusion score. SignalP-NN (neural network) provides four scores and a conclusion for each such that the conclusion is 1 if the score meets a certain criteria and 0 otherwise. The SignalP summary conclusion is the sum of the four conclusions generated by SignalP, thus four is the highest score possible. We consider a summary conclusion score of three to be significant.
ITPPR
ITPPR
min sigp sum score
minimum signalp probability setting specification
A software execution setting specification that specifies the minimum value of signal probability from SignalP-HMM.
ITPPR
ITPPR
min sigp signal probability
any or all signalp setting specification
A software execution setting specification that specifies Union or intersection of advanced parameters.
ITPPR
ITPPR
find genes objective
An objective specification of retrieving genes based on different parameters (e.g., gene locus tag, taxonomy or signal peptide etc.).
ITPPR
ITPPR
find genes by taxonomy execution
A web service execution that retrieves all genes of one or more species/organism(s).
ITPPR
ITPPR
gene locus tag
A CRID symbol that is systematically applied to every gene in a genome within the context of sequencing projects.
Gene ID
ITPPR
EMBL-EBI
RNA sequence data
A sequence data that is about the primary structure of RNA.
ITPPR
ITPPR
coding sequence data
A sequence data that is about primary structure of coding sequence of DNA.
Coding Sequence
ITPPR
ITPPR
protein sequence length
A data item that represents length of predicted protein sequence.
ITPPR
ITPPR
Protein Length.
find genes using signal peptide execution
A web service execution that retrieves all genes that are predicted to encode a signal peptide.
ITPPR
ITPPR
genomic location of gene
ITPPR
A data item indicates the location of a gene in the genome, which can influence the expression of the gene and functional interactions of the gene expression products.
CBIL-UPENN
For a gene identified by gene locus tag TGME49_039250 the corresponsing genomic location of the gene would be TGME49_chrVI: 484,995 - 494,025 (-) where 484,995 is the starting position and 494,025 is the end position of the gene in the genome data.
location text
find genes by locus tag execution
A web service execution that retrieves genes using list of comma separated gene locus tag.
ITPPR
ITPPR
maximum isoelectric point setting secification
A software execution setting specification that specifies the upper bound for the protein isoelectric point.
ITPPR
ITPPR
maximum isoelectric point
minimum number of predicted transmembrane domains setting specification
A software execution setting specification that specifies the lower bound on number of predicted transmembrane domains a protein may have.
ITPPR
ITPPR
minimum number of predicted transmembrane domains
minimum isoelectric point setting specification
A software execution setting specification that specifies the lower bound for the protein isoelectric point.
ITPPR
ITPPR
minimum isoelectric point
epitope confidence setting specification
A software execution setting specification that specifies the confidence of epitope present in predicted protein for a gene. This parameter can have combination High, Medium or Low as values.
ITPPR
ITPPR
The epitope confidence can be specified as High, Medium or Low.
epitope confidence
find genes by transmembrane domain execution
A web service execution that retrieves all genes having number of predicted transmembrane domains in a range that user specify.
ITPPR
ITPPR
find genes by transmembrane domain
find genes with epitopes execution
A web service execution that retrieves all genes whose encoding protein has an epitope identified by the Immune Epitope Database and Analysis Resource with the confidence specified by the user.
ITPPR
ITPPR
find genes with epitopes
find genes by molecular weight execution
A web service execution that retrieves all genes whose unmodified protein product has a molecular weight in a range that user specify.
ITPPR
ITPPR
find genes by molecular weight
minimum molecular weight setting specification
A software execution setting specification that specifies the minimum value for protein molecular weight.
ITPPR
ITPPR
minimum molecular weight
maximum molecular weight setting specification
A software execution setting specification that specifies the maximum value for protein molecular weight.
ITPPR
ITPPR
maximum molecular weight
maximum number of predicted transmembrane domains setting specification
A software execution setting specification that specifies the upper bound on number of predicted transmembrane domains a protein may have.
ITPPR
ITPPR
maximum number of predicted transmembrane domains
find genes by isoelectric point execution
A web service execution that retrieves all genes whose protein product has an isoelectric point in a range that user specify.
ITPPR
ITPPR
find genes by isoelectric point
region
primary structure of sequence macromolecule
sequence
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
region
polypeptide
polypeptide sequence
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
polypeptide
polymer_attribute
http://purl.obolibrary.org/obo/so.owl
An attribute to describe the kind of biological sequence.
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
organizational term
PERSON:Alan Ruttenberg
term created to ease viewing/sort terms for development purpose, and will not be included in a release
ready for release
Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor.
to be replaced with external ontology term
Alan Ruttenberg
Terms with this status should eventually replaced with a term from another ontology.
group:OBI
requires discussion
A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues.
Alan Ruttenberg
group:OBI
PAM
BLOSUM62
20
absolute
both
percent
BLASTp
A BLAST algorithm that searches/aligns a protein query sequence against a protein database at a protein level.
BLASTx
A BLAST algorithm that searches/aligns a nucleotide query sequence against a protein database at a protein level.
BLASTn
A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a nucleotide level.
FASTA
aligned
Poisson
bottom
input
kap
sump
high
seg+xnu
tBLASTn
A BLAST algorithm that searches/aligns a protein query sequence against a nucleotide database at a protein level.
top
low
seg
xnu
medium
tBLASTx
A BLAST algorithm that searches/aligns a nucleotide query sequence against a nucleotide database at a protein level.
normal