IRC log of hcls on 2009-10-15
Timestamps are in UTC.
- 15:00:04 [RRSAgent]
- RRSAgent has joined #hcls
- 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]
- andreasplendiani has joined #HCLS
- 15:03:20 [mscottm]
- I'm in channel "HCLS". Just talked to Alan Hobbs.
- 15:03:27 [jluciano]
- jluciano has joined #hcls
- 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]
- michel has joined #HCLS
- 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]
- matthias_samwald has left #hcls
- 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
- 16:10:46 [bbalsa]
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- 17:30:25 [Zakim]
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