Ontology Summit 2007: OntologySummit2007_Survey individual responses

OntologySummit2007_Survey/Response input from Olivier Bodenreider

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

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Question 1 Respondant Info

Name: Olivier Bodenreider

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

[ ] Formal ontology communities

[ ] Semantic Web communities

[ ] Linguistic communities

[ ] Concept Map community

[ ] Topic Map community

[ ] SEARCH communities

[ ] Web 2.0 communities

[ ] Thesauri community

[ ] Taxonomy communities

[ ] Metadata communities

[ ] XML communities

[ ] Applications Development, Software Engineering and Information Model communities

[ ] System Architecture communities

[X] Biomedical communities

[ ] Standards Development communities

[ ] Other (please specify): (Not Answered)

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

[X] 14. Biomedical communities

[ ] 15. Standards Development communities

[ ] 16. Other (please specify): (Not Answered)

Question 2b Specific Community

or sub-community I am affiliated with: (Not Answered)

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): (Not Answered)

Question 3a Ontology Value -

"1) A reference for entities of biomedical interest (e.g., for indexing

and annotation purposes)

2) A source of relations among biomedical entities (close to knowledge bases)"

Question 3b Ontology Issues -

"- disconnect between ontology artifacts / approaches and practical problems

- lack of distinction between various things called ontologies"

Question 3c Ontology Problems -

"- completeness

- consistency

- interoperability / integration

- lack of an identifying scheme for biomedical entities"

Question 3d Corresponding Solutions -

"- methods / metrics for evaluating ontologies

- methods for automatic acquisition of ontologies (e.g., from text corpora)

- reference ontologies, upper-level ontologies"

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

Term: controlled vocabulary / thesaurus

Gloss: The Metathesaurus is a very large, multi-purpose, and multi-lingual

vocabulary database that contains information about biomedical and

health related concepts, their various names, and the

relationships among them.

Reference (citation/url): http://www.nlm.nih.gov/research/umls/meta2.html

Artifact (name/version): Unified Medical Language System (UMLS) Metathesaurus

- Artifact Ref. (url): http://umlsks.nlm.nih.gov/

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

[X] 3. 3 - sometimes

[ ] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4a2 Additional Remarks -

"NLM itself does not use the word ontology to refer to the UMLS Metathesaurus,

but more and more of its users do."

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

Term: Semantic network

Gloss: The Semantic Network consists of (1) a set of broad subject

categories, or Semantic Types, that provide a consistent

categorization of all concepts represented in the

UMLS Metathesaurus, and (2) a set of useful and

important relationships, or Semantic ...

Reference (citation/url): http://www.nlm.nih.gov/research/umls/meta3.html

Artifact (name/version): Unified Medical Language System (UMLS) Semantic Network

- Artifact Ref. (url): http://umlsks.nlm.nih.gov/

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

[X] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4b2 Additional Remarks -

"Of the 3 knowledge sources in the UMLS, the Semantic Network is the

closest to an ontology. It has been proposed as an upper-level ontology

for the biomedical domain."

Question 4cGlossary - 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 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

[ ] 5. 5 - almost always

Question 4c2 Additional Remarks -

"(Not Answered)"

Question 4dGlossary - 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 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

[ ] 5. 5 - almost always

Question 4d2 Additional Remarks -

"(Not Answered)"

Question 4eGlossary - 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 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

[ ] 5. 5 - almost always

Question 4e2 Additional Remarks -

"(Not Answered)"

Question 4fGlossary - 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 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

[ ] 5. 5 - almost always

Question 4f2 Additional Remarks -

"(Not Answered)"

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

Term: (Not Answered)

Gloss (definition): (Not Answered)

Reference (citation/url): (Not Answered)

Artifact (name/version): (Not Answered)

- 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

[ ] 5. 5 - almost always

Question 4g2 Additional Remarks -

"(Not Answered)"

Question 4hGlossary - 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 5a Co-Sponsor confirmation:

Organization Name: National Library of Medicine

Link (url) to Logo: http://www.nlm.nih.gov/