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Date/Time: Thursday, October 6, 2011; 12-1 PM ET
Lead: Sherri De Coronado
Moderator: Brian Davis

Attendees

Brian Davis, Sherri De Coronado, Hua Min, Stuart Bell, Larry Wright, Trish Whetzel, Rick Kiefer, Riki Ohira

Notes

  • Brian Davis went through the Action Items from the last meeting
    • He contacted Nathan Baker
    • Brian asked Stuart Turner if he's the best point of contact with OMV
    • Some discussion on what Joe Glick and Nathan Baker are doing:  Nanotech or upper level ontology?
    • Stuart and Hua Min suggested other journals that we could publish in
      • We can wait a few weeks before deciding on which journal to submit
      • Stuart felt we should keep it to the open journals
      • Sherri doesn't have a strong feeling either way
      • Need to consider the budget and how much submission of an article would cost (charges for publication)
      • Later we can discuss more in depth a journal
      • Journals:
        • Journal of Biomedical Informatics
        • International Journal of Metadata, Semantics and Ontologies
        • Journal of Information Science
        • Computational Science & Discovery
        • Journal of Biomedical Semantics
        • BMC Bioinformatics
        • PLOS Computational Biology

Journal name

Impact Factor (2002-2009)

2010

Open Access?

Bioinformatics

6.5

5.0

---

BMC Bioinformatics

4.2

---

Yes: http://www.biomedcentral.com/bmcbioinformatics Exit Disclaimer logo

Genome Biology

7.8

---

---

Genome Research

9.7

---

---

Current Bioinformatics

1.3

---

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Proteins: Structure Function and Bioinformatics

4.0

---

---

PLOS Computational Biology

6.1

---

Yes http://www.ploscompbiol.org/home.action Exit Disclaimer logo

Journal of Computational Biology

2.3

---

---

Nucleic Acids Research

7.0

---

---

Molecular Biosystems

4.5

---

---

Molecular Systems Biology

12.6

---

---

MIS Quarterly

9.8 (2006-2011)

5.0

---

Journal of the America Medical Informatics Association

6.2

---

---

Information Systems Research

5.3

---

---

Journal of Biomedical Semantics (online)

---

---

Yes

Applied Ontology

---

---

---

Computational Science and Discovery

---

---

Yes http://iopscience.iop.org/1749-4699/ Exit Disclaimer logo

  • Hua Min had Action Item to provide a list of caBIG --reviewed terminologies for possible set of terminologies to test in a draft implementation (to present at the end of the call)
  • Sherri worked with Harold on OMV+ and CTS2; shows that CTS2 did use OMV and for the most part maps to OMV. The core elements which weren't many, there is a fairly simple mapping with exception of version. Sherri’s table of comparing OMV to CTS2: core elements look pretty good.
    • Bottom line: while still unsure of a number of elements, it looks pretty close and the differences are not going to keep us from moving forward
    • We shouldn't need to chose between one or the other; CTS 2 will be the one that is implemented and it will have the metadata from OMV
    • Any explicit requirements for CTS 2 should be met
    • Trish: some form of CTS2 will be used in BioPortal.
    • SD: do you have CTS2 impl yet?
    • Trish: Not yet, but going to be coming from info in BioPortal. So it’ll all have to be synchronized (NCBO/CTS2 and OMV). So the bioportal metadata will be transformed into CTS2.
    • SD: right in line with what we are doing here.. So we may not have to choose between one or the other.
    • Trish: yes.
  • Trish Whetzel presented on NCBO’s implementation and plans for ”user reviews” of terminologies/ontologies at Bioportal; how NCBO now treats "Community Reviews"
    • The Browse tab lists all the ontologies and sort by reviews to see which ontologies had the most reviews and includes "reviews" column
    • Can add a Review and is a more simplified data collection "form"; can add as many ratings as you like as well as adding text and usually shows hyperlinks to source documents as an option
    • Organized with the newest reviews are at the top; reviews are mid-way through the page
    • The hope is that once you get critical mass of reviews, the community would be able to comment on other comments to say whether they agree/disagree with other assessments
    • Amazon/Yelp do have "Average" review as an option, which could be considered if this comment review gets to the point of having too many
    • Q: Are you thinking of having rating page on the first page so you can sort by ratings? A: Haven't talked about it yet. It could be done.
    • The metadata included for each ontology
      • Went through the different fields to see if they are similar to OMV
      • Ontology Format was not seen in OMV, unless it was part of the BioPortal extension
      • Need to make sure that metadata fields in BioPortal that aren't in OMV need to add back (make sure they are aligned)
      • Comment: Author isn't really author, it's more like Source or Creator
    • The reviews sent to summary pages about 2-3 months ago; Brian commented that it looks great.
    • Screen shot (stage site and production site): http://bioportal.bioontology.org/ Exit Disclaimer logo
    • Browse tab in BioPortal: http://bioportal.bioontology.org/ontologies Exit Disclaimer logo
    • Look at NCI Thesaurus
    • Shows for SNOMED CT including the VCDE WS review
    • Brian asks if they have thought of putting the ratings (by stars) in the face page, so that people can browse or sort on ratings?
    • Trish to bring it up with NCBO/BioPortal.
    • SD asking questions about what metadata lines up with OMV/CTS2 (for example, “viewing restriction”)
    • Can see it from the “submit new ontology:
    • Put those in table.
  • Hua Min provided list of ontologies/terminologies reviewed by caBIG (for next week)
    • Use it to identify set of ontologies to apply to this core model and need to cross-reference with BioPortal (to make sure they were in both places)
  • Next week:
    • Hua Min can discuss terminologies identified and group can determine which ones to use
    • Sherri can present on finished table (NCBO comparison)

Action Item:

Assigned To

Description

Due Date

Brian

Make Project plan a wiki page

Oct 13

Brian

Make Wiki Page of Possible Journals to publish in

Oct 13

Riki

Make Table of CTS2 to OMV and OMV+ comparison into a table on wiki

Oct 13

Riki

Post Hua Min’s list of Vocabs reviewed in caBIG on wiki

Oct 13

Brian

(carried over another week) Remind people of Poll for Alternative times to meet

Oct 13

Brian

(carried over another week) Ask Stuart for update from OMV leadership

Oct 13

Sherri

(carried over another week) Look at reviews Trish posted to Bioportal abstracted form caBIG VCDE reviews, see if any are missing, etc.

Oct 13

Grace

(carried over another week) Look thru references that Stuart put together and see if any can be applied to NCBO reviews page

Oct 13

Sherri

(carried over another week) Analyze what NCBO has vs. what OMV has (same), and implementation differences

Oct 13

Trish and Brian

Report on Meta-Ontology group activity

Oct 27

Hua Min

Look up more information on the International Journal of Metadata (how well-known is it in the US)

Oct 13

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