IRC log of hcls on 2009-10-15

Timestamps are in UTC.

15:00:04 [RRSAgent]
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15:00:04 [RRSAgent]
logging to http://www.w3.org/2009/10/15-hcls-irc
15:00:15 [curoli]
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15:00:54 [mib_529p54]
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15:01:36 [michaelb]
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15:01:51 [mib_529p54]
I've called into Zakim. No one seems online [Nigam]
15:02:18 [andreasplendiani]
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15:03:20 [mscottm]
I'm in channel "HCLS". Just talked to Alan Hobbs.
15:03:27 [jluciano]
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15:03:41 [mscottm]
Now, I seem to be in a lost channel - will try again!
15:03:44 [kei]
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15:03:58 [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".
15:04:18 [michel]
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15:05:25 [mscottm]
Zakim, who is here?
15:05:25 [Zakim]
sorry, mscottm, I don't know what conference this is
15:05:27 [Zakim]
On IRC I see michel, kei, jluciano, andreasplendiani, michaelb, mib_529p54, curoli, RRSAgent, Zakim, bbalsa, mscottm, matthias_samwald, ahobbs, egonw, ericP, Cloud, AlexPassant
15:05:47 [mscottm]
Zakim, mib_529p54 is NigamShah
15:05:47 [Zakim]
sorry, mscottm, I do not recognize a party named 'mib_529p54'
15:06:00 [mscottm]
Zakim, mib_529p54 is NigamShah
15:06:00 [Zakim]
sorry, mscottm, I do not recognize a party named 'mib_529p54'
15:06:16 [mib_529p54]
mib_529p54 is Nigam Shah
15:07:10 [mib_529p54]
https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0
15:07:37 [mscottm]
Zakim, this will be HCLS
15:07:37 [Zakim]
ok, mscottm, I see SW_HCLS()11:00AM already started
15:07:43 [mscottm]
Zakim, who is here?
15:07:43 [Zakim]
On the phone I see +1.510.802.aaaa, ??P34, ??P40, +1.617.993.aacc, +46.4.63.3.aadd, Kei_Cheung, +1.585.919.aaee, +1.617.818.aaff
15:07:45 [Zakim]
On IRC I see michel, kei, jluciano, andreasplendiani, michaelb, mib_529p54, curoli, RRSAgent, Zakim, mscottm, matthias_samwald, ahobbs, egonw, ericP, Cloud, AlexPassant
15:09:18 [mscottm]
Scribenick: jluciano
15:11:05 [Zakim]
+ +0754501aagg
15:11:48 [mscottm]
Zakim, +0754501aagg is andreassplendiani
15:11:49 [Zakim]
+andreassplendiani; got it
15:12:50 [Zakim]
+??P10
15:12:57 [jluciano]
Nigham Shah presentation
15:13:11 [jluciano]
talking primarily about web services (focus)
15:13:34 [mscottm]
https://stanford.webex.com/mc0805l/meetingcenter/docshow/docframe.do?siteurl=stanford&Rnd=9651951
15:13:51 [Zakim]
+ +1.860.255.aahh
15:13:55 [mib_529p54]
https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0
15:13:56 [mscottm]
https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0
15:14:06 [jluciano]
Presentation: Using NCBO Web Services / National Center for Biomedical Ontology
15:14:50 [jluciano]
What NCBO does - 3 things: create and maintain library of biomedical ontologies
15:15:09 [jluciano]
Build tools and WEB SERVICES to enable use of Ontologies
15:15:32 [jluciano]
Collaborate with scientific communities that develop and use ontologies
15:16:08 [jluciano]
multiple types of collaborations - grants, seminars, ....
15:16:21 [mscottm]
collab with Barry Smith
15:16:28 [jluciano]
Home page: bioontology.org
15:17:03 [jluciano]
Ontology Services - 3 kinds
15:17:25 [jluciano]
(1) for access browwsing, searching, transversing, in YOUR app --> ontology services
15:17:43 [jluciano]
there's a list of the servicces -
15:18:22 [jluciano]
Nigam will getting, searching and finding details and then traversing the hierarchies --- things sw app might need to do
15:18:39 [jluciano]
rest.bioontology.org/<service name>
15:19:21 [jluciano]
back end (and independent access to resources avaiable)
15:19:37 [jluciano]
MeSH example
15:20:00 [jluciano]
Ontology ID is most useful. gives refernce
15:20:18 [jluciano]
Translation gives the identifier name space
15:20:35 [Zakim]
- +1.585.919.aaee
15:20:50 [mscottm]
Zakim just hung up on me :(
15:20:51 [jluciano]
next service cal is mesh, ex. "melanoma"
15:20:55 [jluciano]
:-(
15:20:58 [Zakim]
+ +1.585.919.aaii
15:21:02 [mscottm]
I'm back. :)
15:21:18 [mscottm]
Zakim, +1.585.919.aaii is mscottm
15:21:18 [Zakim]
+mscottm; got it
15:21:20 [jluciano]
1351 is the Mesh Identifier
15:21:49 [jluciano]
Long --> full URI short --> name
15:22:00 [jluciano]
not all ontologies give full URI
15:22:06 [jluciano]
then the short and long are the same
15:23:05 [jluciano]
get back a list of properties (Note: concept unique identifier == "CUI))
15:23:22 [jluciano]
mesh doesn't provide URI
15:23:46 [jluciano]
so currently can't get full URIs
15:25:29 [jluciano]
how you do it:
15:26:47 [mscottm]
tx Joanne
15:26:59 [jluciano]
service listed on wiki -
15:27:11 [jluciano]
this is a rest service, it's like accessign a URL
15:27:49 [jluciano]
the example gets the semantic type out of the ??? service
15:28:11 [jluciano]
1) get list
15:28:15 [jluciano]
2) seaerch any subset
15:28:27 [jluciano]
3) once pick, can get details, parent, sibling nodes, etc.
15:28:36 [jluciano]
4) gets hierarchy to root
15:28:58 [jluciano]
next service: annotator -- using ontology to annotate *you* data
15:29:12 [jluciano]
most common use - to annotate datasets
15:29:30 [jluciano]
automatically tag text (for example)
15:30:12 [jluciano]
parse text (via userinterface: http://bioportal.bioontology.org/annotate
15:30:22 [jluciano]
results come back as tab delimited text or xml
15:30:48 [jluciano]
give your text as input, select your parameters, get xml results in text or XML
15:34:03 [mscottm]
http://code.google.com/apis/opensocial/
15:35:35 [kei]
e-utils at ncbi
15:35:41 [jluciano]
third part - access already existing throug etils, and ohter
15:35:42 [Zakim]
+ +1.317.277.aajj
15:36:07 [mscottm]
https://stanford.webex.com/stanford/j.php?ED=123032982&UID=1135545127&PW=NZjg2MjkzZjQw&RT=MiM0
15:36:17 [mscottm]
Please see above link for webex session.
15:36:23 [jluciano]
eUtils used for NCBI, some groups rest, some FTP some dowload access
15:36:46 [Christi]
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15:37:25 [jluciano]
the index (Open Biomedical Resoruces (OBR) index) used for search/data mining
15:37:36 [mib_s7cwlb]
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15:38:26 [jluciano]
example, accessiming resource elements, concept recognition, semantic expansion, closure
15:38:34 [jluciano]
85-95 accurate for disease
15:38:47 [jluciano]
drug lower precision
15:38:56 [jluciano]
body parts
15:39:12 [jluciano]
paper at AMIA presented by Nigham
15:39:18 [jluciano]
fully automated
15:39:52 [mscottm]
Using the Stanford Parser to boost the confidence of annotation with syntax tree info
15:39:56 [jluciano]
rest.biooltology.org/resource_index/<service> ---> 15 sevices surrently
15:40:34 [jluciano]
(scott, thanks for the assist!)
15:41:16 [jluciano]
example - Gene Cfl1, get some text, another gene, than take these and "push them to the annotator"
15:41:24 [jluciano]
get spina bifita (disease result)
15:41:39 [jluciano]
turn text desc to ont term definitinos
15:42:15 [jluciano]
way to find bioprocess or component (gene enrighment)
15:44:01 [jluciano]
see webiste for wiki page on how to use NCBO services in your project
15:44:29 [jluciano]
"teaser" grant title, NCI thesaurus, which grants have which genes have which dollar amounts
15:44:48 [jluciano]
creates graphic - showing receptor genes studied a lot
15:44:59 [jluciano]
a lot of funding gone to few genes
15:45:30 [jluciano]
suggest using eHR and see if a hosp is getting disproportionate of TB, for exmaple
15:45:56 [mib_529p54]
http://www.stanford.edu/~nigam/download
15:45:56 [jluciano]
Mark Musenl PU, team @ bioontology.org
15:46:42 [jluciano]
NIH Roadmap grant U54 HG004028
15:47:04 [jluciano]
kei: what if term not found?
15:47:44 [jluciano]
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)
15:49:18 [jluciano]
kei: re: expansion, if term deep in hierarchy, does exapsion increase time? Nigam - it's precomoputed, but mapping does increase time
15:49:42 [jluciano]
can the level of expansion be difined? Nigham: yues, and show it in demo
15:50:03 [jluciano]
go to annotate tab, amongst options, there is a setting for maiximum level
15:58:17 [Zakim]
- +1.317.277.aajj
15:58:34 [Zakim]
- +1.860.255.aahh
15:58:41 [Zakim]
- +1.510.802.aaaa
16:01:11 [jluciano]
sorry ---> Have to go to another (hcls call now)
16:01:56 [Zakim]
-??P10
16:02:33 [Zakim]
- +46.4.63.3.aadd
16:02:38 [Zakim]
-??P34
16:02:41 [andreasplendiani]
bye!
16:02:43 [Zakim]
-Kei_Cheung
16:03:00 [Zakim]
-andreassplendiani
16:03:05 [Zakim]
-??P40
16:03:32 [Christi]
Christi has left #hcls
16:03:44 [Zakim]
-mscottm
16:03:46 [Zakim]
- +1.617.993.aacc
16:03:54 [Zakim]
- +1.617.818.aaff
16:03:56 [Zakim]
SW_HCLS()11:00AM has ended
16:03:59 [Zakim]
Attendees were +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,
16:04:06 [Zakim]
... +1.317.277.aajj
16:04:58 [matthias_samwald]
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16:05:11 [mscottm]
RRSAgent, please draft minutes
16:05:11 [RRSAgent]
I have made the request to generate http://www.w3.org/2009/10/15-hcls-minutes.html mscottm
16:05:22 [mscottm]
RRSAgent, please make log world-visible
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