HCLSIG/Meetings/2009-10-15 Conference Call
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- 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 #: +33.4.89.06.34.99 (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
- Using NCBO Web Services / National Center for Biomedical Ontology - Nigam Shah, see also BioPortal.
- 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".
- Next F2F - All
- Provenance Incubator Group - Scott
15 Oct 2009
See also: IRC log Attendees
- 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
<mscottm> Scribenick: jluciano
Nigham Shah presentation
talking primarily about web services (focus)
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
back end (and independent access to resources avaiable)
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
<kei> e-utils at ncbi
third part - access already existing throug etils, and ohter
<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
paper at AMIA presented by Nigham
<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
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)