See also: IRC log
<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!
This is scribe.perl Revision: 1.135 of Date: 2009/03/02 03:52:20 Check for newer version at http://dev.w3.org/cvsweb/~checkout~/2002/scribe/ Guessing input format: RRSAgent_Text_Format (score 1.00) Found ScribeNick: jluciano Inferring Scribes: jluciano WARNING: No "Topic:" lines found. Default Present: +1.510.802.aaaa, +1.585.919.aabb, +1.617.993.aacc, +46.4.63.3.aadd, Kei_Cheung, +1.585.919.aaee, +1.617.818.aaff, andreassplendiani, +1.860.255.aahh, mscottm, +1.317.277.aajj Present: +1.510.802.aaaa +1.585.919.aabb +1.617.993.aacc +46.4.63.3.aadd Kei_Cheung +1.585.919.aaee +1.617.818.aaff andreassplendiani +1.860.255.aahh mscottm +1.317.277.aajj WARNING: No meeting title found! You should specify the meeting title like this: <dbooth> Meeting: Weekly Baking Club Meeting WARNING: No meeting chair found! You should specify the meeting chair like this: <dbooth> Chair: dbooth Got date from IRC log name: 15 Oct 2009 Guessing minutes URL: http://www.w3.org/2009/10/15-hcls-minutes.html People with action items: WARNING: Input appears to use implicit continuation lines. You may need the "-implicitContinuations" option. WARNING: No "Topic: ..." lines found! Resulting HTML may have an empty (invalid) <ol>...</ol>. Explanation: "Topic: ..." lines are used to indicate the start of new discussion topics or agenda items, such as: <dbooth> Topic: Review of Amy's report[End of scribe.perl diagnostic output]