HCLSIG/Meetings/2009-10-15 Conference Call

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Conference Details

  • Date of Call: Thursday October 15, 2009
  • Time of Call: 11:00am Eastern Daylight Time (EDT), 16:00 British Summer Time (BST), 17:00 Central European Time (CET)
  • Dial-In #: +1.617.761.6200 (Cambridge, MA)
  • Dial-In #: + (Nice, France)
  • Dial-In #: +44.117.370.6152 (Bristol, UK)
  • Participant Access Code: 4257 ("HCLS").
  • IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for details, or see Web IRC), Quick Start: Use mibbit for IRC access.
  • Duration: ~1h
  • Convener: Scott, Susie
  • Scribe: TBD



15 Oct 2009

See also: IRC log Attendees






  • Topics
  • Summary of Action Items

<mib_529p54> I've called into Zakim. No one seems online [Nigam]

<mscottm> I'm in channel "HCLS". Just talked to Alan Hobbs.

<mscottm> Now, I seem to be in a lost channel - will try again!

<mib_529p54> 1. Go to https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0 2. Enter your name and email address. 3. Enter the meeting password: ncbomeeting 4. Click "Join Now".

<mib_529p54> mib_529p54 is Nigam Shah

<mib_529p54> https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0

<mscottm> Scribenick: jluciano

Nigham Shah presentation

talking primarily about web services (focus)

<mscottm> https://stanford.webex.com/mc0805l/meetingcenter/docshow/docframe.do?siteurl=stanford&Rnd=9651951

<mib_529p54> https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0

<mscottm> https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0

Presentation: Using NCBO Web Services / National Center for Biomedical Ontology

What NCBO does - 3 things: create and maintain library of biomedical ontologies

Build tools and WEB SERVICES to enable use of Ontologies

Collaborate with scientific communities that develop and use ontologies

multiple types of collaborations - grants, seminars, ....

<mscottm> collab with Barry Smith

Home page: bioontology.org

Ontology Services - 3 kinds

(1) for access browwsing, searching, transversing, in YOUR app --> ontology services

there's a list of the servicces -

Nigam will getting, searching and finding details and then traversing the hierarchies --- things sw app might need to do

rest.bioontology.org/<service name>

back end (and independent access to resources avaiable)

MeSH example

Ontology ID is most useful. gives refernce

Translation gives the identifier name space

<mscottm> Zakim just hung up on me :(

next service cal is mesh, ex. "melanoma"


<mscottm> I'm back. :)

1351 is the Mesh Identifier

Long --> full URI short --> name

not all ontologies give full URI

then the short and long are the same

get back a list of properties (Note: concept unique identifier == "CUI))

mesh doesn't provide URI

so currently can't get full URIs

how you do it:

<mscottm> tx Joanne

service listed on wiki -

this is a rest service, it's like accessign a URL

the example gets the semantic type out of the ??? service

1) get list

2) seaerch any subset

3) once pick, can get details, parent, sibling nodes, etc.

4) gets hierarchy to root

next service: annotator -- using ontology to annotate *you* data

most common use - to annotate datasets

automatically tag text (for example)

parse text (via userinterface: http://bioportal.bioontology.org/annotate

results come back as tab delimited text or xml

give your text as input, select your parameters, get xml results in text or XML

<mscottm> http://code.google.com/apis/opensocial/

<kei> e-utils at ncbi

third part - access already existing throug etils, and ohter

<mscottm> https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0

<mscottm> Please see above link for webex session.

eUtils used for NCBI, some groups rest, some FTP some dowload access

the index (Open Biomedical Resoruces (OBR) index) used for search/data mining

example, accessiming resource elements, concept recognition, semantic expansion, closure

85-95 accurate for disease

drug lower precision

body parts

paper at AMIA presented by Nigham

fully automated

<mscottm> Using the Stanford Parser to boost the confidence of annotation with syntax tree info

rest.biooltology.org/resource_index/<service> ---> 15 sevices surrently

(scott, thanks for the assist!)

example - Gene Cfl1, get some text, another gene, than take these and "push them to the annotator"

get spina bifita (disease result)

turn text desc to ont term definitinos

way to find bioprocess or component (gene enrighment)

see webiste for wiki page on how to use NCBO services in your project

"teaser" grant title, NCI thesaurus, which grants have which genes have which dollar amounts

creates graphic - showing receptor genes studied a lot

a lot of funding gone to few genes

suggest using eHR and see if a hosp is getting disproportionate of TB, for exmaple

<mib_529p54> http://www.stanford.edu/~nigam/download

Mark Musenl PU, team @ bioontology.org

NIH Roadmap grant U54 HG004028

kei: what if term not found?

not through annotator - but if submitted paragraph, then can go to human disease ontology page and give feedback (but can't do it automatically at this time)

kei: re: expansion, if term deep in hierarchy, does exapsion increase time? Nigam - it's precomoputed, but mapping does increase time

can the level of expansion be difined? Nigham: yues, and show it in demo

go to annotate tab, amongst options, there is a setting for maiximum level

sorry ---> Have to go to another (hcls call now)

<andreasplendiani> bye!