Ontology Summit 2007: OntologySummit2007_Survey individual responses

OntologySummit2007_Survey/Response input from Ken Baclawski

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: Ken Baclawski

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

[ ] Metadata communities

[ ] XML communities

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

[ ] System Architecture communities

[X] Biomedical communities

[X] 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: bioinformatics, biodiversity

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 -

"Ontologies are used for improved patient care, health services billing,

public health records/statistics, indexing and cataloging biomedical

literature, basic research, clinical research, and health services research."

Question 3b Ontology Issues -

"1. Very large number of formats

2. Lack of ontological engineers

3. Tool incompatibilities"

Question 3c Ontology Problems -

"Representing uncertain facts"

Question 3d Corresponding Solutions -

"See the meeting at http://colab.cim3.net/cgi-bin/wiki.pl?OpenGroupSICoP_2006_04_27"

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

Term: Thesaurus

Gloss: hierarchical, equivalence and associative relationships among concepts

Reference (citation/url): http://agclass.nal.usda.gov/agt/relationships.shtml

Artifact (name/version): National Agricultural Library Thesaurus (NALT)

- Artifact Ref. (url): http://agclass.nal.usda.gov/agt/download.shtml

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 -

"Online vocabulary look-up tool for agricultural and biological terms"

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

Term: Controlled vocabulary thesaurus

Gloss: It consists of sets of terms naming descriptors in a hierarchical structure

that permits searching at various levels of specificity

Reference (citation/url): http://www.nlm.nih.gov/pubs/factsheets/mesh.htm

Artifact (name/version): Medical Subject Headings (MeSH)

- Artifact Ref. (url): http://www.nlm.nih.gov/mesh/termscon.html

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 -

"The MeSH thesaurus is used by NLM for indexing articles from 4,800 of

the world's leading biomedical journals for the MEDLINE/[[PubMED]] database.

It is also used for the NLM-produced database that includes cataloging of

books, documents, and audiovisuals acquired by the Library. Each bibliographic

reference is associated with a set of MeSH terms that describe the content of the

item. Similarly, search queries use MeSH vocabulary to find items on a desired topic."

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

Term: Metathesaurus

Gloss: Vocabulary database. The term Metathesaurus draws on

Webster's Dictionary third definition for the prefix "meta,"

i.e., "more comprehensive, transcending." In a sense, the

Metathesaurus transcends the specific thesauri, vocabularies, and classificatio...

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

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

- Artifact Ref. (url): http://www.nlm.nih.gov/research/umls/access.html

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

[X] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4c2 Additional Remarks -

"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. Designed for use by system developers, the Metathesaurus

is built from the electronic versions of various thesauri, classifications,

code sets, and lists of controlled terms used in patient care, health

services billing, public health statistics, indexing and cataloging

biomedical literature, and/or basic, clinical, and health services research.

These are referred to as the "source vocabularies" of the Metathesaurus."

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

Term: Semantic network

Gloss: (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 Relations,

that exist between Sem...

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

Artifact (name/version): UMLS Semantic Network

- Artifact Ref. (url): http://www.nlm.nih.gov/research/umls/access.html

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

[X] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4d2 Additional Remarks -

"The purpose of the Semantic Network is to provide a consistent categorization

of all concepts represented in the UMLS Metathesaurus and to provide a set

of useful relationships between these concepts."

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

Term: Ontology

Gloss: (Not Answered)

Reference (citation/url): (Not Answered)

Artifact (name/version): Gene Ontology (GO)

- Artifact Ref. (url): http://archive.geneontology.org/latest-termdb/go_daily-termdb.rdf-xml.gz

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 -

"The GO project has developed three structured controlled vocabularies (ontologies)

that describe gene products in terms of their associated biological processes,

cellular components and molecular functions in a species-independent manner.

There are three separate aspects to this effort: first, the development and

maintenance of the ontologies themselves; second, the annotation of gene products,

which entails making associations between the ontologies and the genes and gene

products in the collaborating databases; and third, development of tools that

facilitate the creation, maintenance and use of ontologies."

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

Term: Ontology

Gloss: (Not Answered)

Reference (citation/url): (Not Answered)

Artifact (name/version): Sequence Ontology (SO)

- Artifact Ref. (url): http://song.cvs.sourceforge.net/song

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 -

"The Sequence Ontology Project (SO) is a joint effort by genome annotation

centres, including: WormBase, the Berkeley Drosophila Genome Project,

FlyBase, the Mouse Genome Informatics group, and the Sanger Institute,

We are a part of the Gene Ontology Project and our aim is to develop

an ontology suitable for describing biological sequences."

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

Term: Ontology

Gloss (definition): Computer-readable, precise formulations of concepts

(and the relationship among them) in a given field.

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

Artifact (name/version): Bayesian Web

- 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 -

"The Bayesian Web is a proposal to add reasoning about certainty

to the Semantic Web"

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

Term: Classification

Gloss: (Not Answered)

Reference (citation/url): (Not Answered)

Artifact (name/version): International Classification of Diseases Version 10 (ICD-10)

- Artifact Ref. (url): http://www.who.int/classifications/icd/en/

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

[X] 2. 2 - rarely

[ ] 3. 3 - sometimes

[ ] 4. 4 - quite often

[ ] 5. 5 - almost always

Question 4h2 Additional Remarks -

"The ICD has become the international standard diagnostic classification

for all general epidemiological and many health management purposes.

These include the analysis of the general health situation of

population groups and monitoring of the incidence and prevalence

of diseases and other health problems in relation to other variables

such as the characteristics and circumstances of the individuals affected.

It is used to classify diseases and other health problems recorded on

many types of health and vital records including death certificates and

hospital records. In addition to enabling the storage and retrieval of

diagnostic information for clinical and epidemiological purposes, these

records also provide the basis for the compilation of national mortality

and morbidity statistics by WHO Member States."

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: (Not Answered)

Link (url) to Logo: (Not Answered)

---