OntologySummit2007 Survey/OlivierBodenreider

= OntologySummit2007: OntologySummit2007_Survey individual responses =

OntologySummit2007_Survey/Response input from OlivierBodenreider
'Please make sure you refer to the OntologySummit2007 &amp; OntologySummit2007_Survey pages for the full context of the input. '

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 OntologySummit2007 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 OntologySummit2007,

[ ]  I agree that my name can be listed as a 'convener' of OntologySummit2007 [ ]  I will consider endorsing the OntologySummit2007 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 OntologySummit2007 (details below).

Question 5a Co-Sponsor confirmation:

Organization Name: National Library of Medicine Link (url) to Logo: http://www.nlm.nih.gov/