Ontology Summit 2007: OntologySummit2007_Survey individual responses

OntologySummit2007_Survey/Response input from Suzi Lewis

Please make sure you refer to the Ontology Summit 2007 & OntologySummit2007_Survey pages for the full context of the input.   

---

Question 1 Respondant Info

Name: Suzanna Lewis

Question 2 Affiliated - I am affiliated with the following constituencies/communities (please check all that apply)

[X] Formal ontology communities

[X] Semantic Web communities

[ ] Linguistic communities

[ ] Concept Map community

[ ] Topic Map community

[ ] SEARCH communities

[ ] Web 2.0 communities

[ ] Thesauri community

[ ] Taxonomy communities

[X] Metadata communities

[ ] XML communities

[X] Applications Development, Software Engineering and Information Model communities

[ ] System Architecture communities

[X] Biomedical communities

[ ] Standards Development communities

[X] Other (please specify): Genomics

Question 2a Representing - I represent the perspective of the following constituency/community (please pick one; if you want to provide input from more than one perspective, please return a separate form):

[ ] 1. Formal ontology communities

[ ] 2. Semantic Web communities

[ ] 3. Linguistic communities

[ ] 4. Concept Map community

[ ] 5. Topic Map community

[ ] 6. SEARCH communities

[ ] 7. Web 2.0 communities

[ ] 8. Thesauri community

[ ] 9. Taxonomy communities

[ ] 10. Metadata communities

[ ] 11. XML communities

[ ] 12. Applications Development, Software Engineering and Information Model communities

[ ] 13. System Architecture communities

[ ] 14. Biomedical communities

[ ] 15. Standards Development communities

[X] 16. Other (please specify): Genomics

Question 2b Specific Community

or sub-community I am affiliated with: Biomedical researchers, Basic researchers, clinical researchers, computational biologists, bioinformaticians, ontologists, philosophers, and systems biologists

Question 2c Expertise Self Assessment - With respect to the perspective you are representing and providing input from, I am a/an:

[ ] 1. informed layman

[ ] 2. practitioner

[X] 3. expert

[ ] 4. other (please specify)

Question 2c Expertise Self Assessment - Specified

other (please specify): (Not Answered)

Question 3a Ontology Value

"Data interoperability: The representation of biological knowledge in databases is a necessity for modern biomedical research. Historically, there has been very little collaboration or coordination between different database providers. Although many grandiose schemes for the "integration" of biological data-bases have been proposed over the years, none have been practical to the point of implementation. Yet the need for integration remains, as many biologists, both those at the bench and those who analyse data computationally, wish to integrate data from a diversity of sources. The Gene Ontology Consortium (GOC) began, some several years ago, to develop a resource that could be used by both the model organism databases (e.g. FlyBase, WormBase, Mouse Genome Da-tabase, The Arabidopsis Information Resource) and the large "horizontal" databases (e.g. Uni-Prot, GeneDB, TIGR Gene Index) as a standard for the annotation of gene products. Out of this experience aros e the Open Biomedical Ontologies (OBO) Foundry collaboration whose goal is to produce well-structured vocabularies for shared use across different biological and medical domains. Those involved agree in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain."

Question 3b Ontology Issues

"1. The annotation bottleneck 2. Sustained maintenance of the requisite ontologies 3. Communications with the other communities listed above"

Question 3c Ontology Problems

"(Not Answered)"

Question 3d Corresponding Solutions

"(Not Answered)"

Question 4a Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: ontology

Gloss: A machine interpretable representation of some aspect of biological reality: the entities that exist and the relationships between them

Reference (citation/url): (Not Answered)

Artifact (name/version): (Not Answered)

- Artifact Ref. (url): (Not Answered)

Question 4a1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4a2 Additional Remarks -

"(Not Answered)"

Question 4b Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Gene Ontology

Gloss: The GO describes gene products in terms of their associated biological processes, cellular components and molecular functions in a species-independent manner.

Reference (citation/url): http://www.geneontology.org/

Artifact (name/version): GO

- Artifact Ref. (url): http://www.geneontology.org/GO.downloads.ontology.shtml

Question 4b1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4b2 Additional Remarks -

"(Not Answered)"

Question 4c Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Sequence Ontology

Gloss: An ontology for describing biological sequences

Reference (citation/url): http://sequenceontology.org/

Artifact (name/version): SO

- Artifact Ref. (url): (Not Answered)

Question 4c1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4c2 Additional Remarks -

"(Not Answered)"

Question 4d Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Phenotype and Trait Ontology

Gloss: This ontology can be used in conjunction with other ontologies such as GO or anatomical ontologies to refer to phenotypes. Examples of qualities are red, ectopic, high temperature, fused, small, edematous and arrested

Reference (citation/url): http://obofoundry.org/cgi-bin/detail.cgi?id=quality&title=Phenotypic%20quality

Artifact (name/version): PATO or quality.obo

- Artifact Ref. (url): (Not Answered)

Question 4d1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4d2 Additional Remarks -

"(Not Answered)"

Question 4e Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Relation Ontology

Gloss: Defines core relations used in all OBO ontologies

Reference (citation/url): http://obofoundry.org/cgi-bin/detail.cgi?id=relationship&title=OBO%20relationship%20types

Artifact (name/version): RO

- Artifact Ref. (url): (Not Answered)

Question 4e1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4e2 Additional Remarks -

"(Not Answered)"

Question 4f Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Common Anatomical Reference Ontology

Gloss: The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies.

Reference (citation/url): http://obofoundry.org/cgi-bin/detail.cgi?id=caro&title=Common%20Anatomy%20Reference%20Ontology

Artifact (name/version): CARO

- Artifact Ref. (url): (Not Answered)

Question 4f1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4f2 Additional Remarks -

"(Not Answered)"

Question 4g Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: Cell Type

Gloss (definition): The Cell Ontology is designed as a structured controlled vocabulary for cell types. This ontology was constructed for use by the model organism and other bioinformatics databases, where there is a need for a controlled vocabulary of cell types. This on...

Reference (citation/url): http://obofoundry.org/cgi-bin/detail.cgi?id=cell&title=Cell%20type

Artifact (name/version): CL

- Artifact Ref. (url): (Not Answered)

Question 4g1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[X] 5. 5 - almost always

Question 4g2 Additional Remarks -

"(Not Answered)"

Question 4h Glossary - Ontology-related 'vocabulary' and representative 'artifact' from your constituency or community:

Term: (Not Answered)

Gloss: (Not Answered)

Reference (citation/url): (Not Answered)

Artifact (name/version): (Not Answered)

- Artifact Ref. (url): (Not Answered)

Question 4h1 Called An Ontology - On a scale of 1 to 5, (where 1 means totally unlikely and 5 means almost always), would the above term or artifact be referred to as an "ontology" in your community?

[ ] 1. 1 - totally unlikely

[ ] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4h2 Additional Remarks -

"(Not Answered)"

Question 5 Confirm Participation - where,

a 'convener' is a participant who provides substantive contribution to the Ontology Summit 2007

initiative (through the online discourse, this survey, and other events leading to or during

the workshops and the written communique process), and

a 'co-sponsor' is an organization who is providing technical or funding support (e.g. supporting

member(s) of its technical staff to participate as a 'convener'), and/or endorsing the objective

of this Ontology Summit 2007,

[ ] I agree that my name can be listed as a 'convener' of Ontology Summit 2007

[ ] I will consider endorsing the Ontology Summit 2007 communique. Please send it to me for

review when it is ready. I will confirm my endorsement after the review.

[ ] I confirm that you may list my organization as a 'co-sponsor' for

Ontology Summit 2007 (details below).

Question 5aCoSponsor

Organization Name: (Not Answered)

Link (url) to Logo: (Not Answered)

---