15:00:04 <RRSAgent> RRSAgent has joined #hcls
15:00:04 <RRSAgent> logging to http://www.w3.org/2009/10/15-hcls-irc
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15:01:36 <michaelb> michaelb has joined #hcls
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> kei has joined #HCLS
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> Christi has joined #hcls
15:37:25 <jluciano> the index (Open Biomedical Resoruces (OBR) index) used for search/data mining
15:37:36 <mib_s7cwlb> mib_s7cwlb has joined #hcls
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
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