Time to start writing -- Bioontologies SIG and Phenotype Day at ISMB/ECCB 2015

Call for Participation for the Bio-Ontologies SIG at ISMB/ECCB 2015 [we will send one more at one week prior to the deadline] *What:* Bio-Ontologies SIG and Phenotype Day *When:* July 10 and July 11, 2015 *Where:* co-located with ISMB/ECCB 2015 in Dublin, Ireland ** Submissions Due: April 10th, 20

One month to submission deadline -- Bioontologies SIG and Phenotype Day at ISMB/ECCB 2015

Call for Participation for the Bio-Ontologies SIG at ISMB/ECCB 2015 [we will send two more at two weeks and one week prior to the deadline] *What:* Bio-Ontologies SIG and Phenotype Day *When:* July 10 and July 11, 2015 *Where:* co-located with ISMB/ECCB 2015 in Dublin, Ireland ** Submissions Due:

57 days to submission deadline -- Bioontologies SIG and Phenotype Day at ISMB/ECCB 2015

Call for Participation for the Bio-Ontologies SIG at ISMB 2015 [we will send three more at one month, two weeks and one week prior to the deadline] *What:* Bio-Ontologies SIG and Phenotype Day *When:* July 10 and July 11, 2015 *Where:* co-located with ISMB/ECCB 2015 in Dublin, Ireland ** Submissio

77 days to submission deadline -- Bioontologies SIG and Phenotype Day at ISMB/ECCB 2015

Call for Participation for the Bio-Ontologies SIG at ISMB 2015 *What:* Bio-Ontologies SIG and Phenotype Day *When:* July 10 and July 11, 2015 *Where:* co-located with ISMB/ECCB 2015 in Dublin, Ireland ** Submissions Due: April 10th, 2015 (Fri) ** *More: *http://www.bio-ontologies.org.uk/call-for-p

Bio-Ontologies Program and early bird deadline (this Friday)

Dear Colleagues, We have about 37 days to go till the 17th Bio-Ontologies meeting at ISMB 2014 in Boston. The final program for 2014 is online at: http://www.bio-ontologies.org.uk/programme and we have a superb line up of papers, flash updates, posters, and a keynote by Melissa Haendel as well as

7 days to submission deadline for the Bio-Ontologies SIG and Phenotype Day at ISMB 2014

The *first* submission came in today (with one week to go!). *Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri)

7 days to submission deadline for the Bio-Ontologies SIG and Phenotype Day at ISMB 2014

The *first* submission came in today (with one week to go!). *Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri)

14 days to submission deadline for the Bio-Ontologies SIG and Phenotype Day at ISMB 2014

*Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri) ** *More*: http://www.bio-ontologies.org.uk/call-for-participa

14 days to submission deadline for the Bio-Ontologies SIG and Phenotype Day at ISMB 2014

*Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri) ** *More*: http://www.bio-ontologies.org.uk/call-for-participa

31 days to submission deadline for the Bio-Ontologies SIG and Phenotype Day at ISMB 2014

*Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri) ** *More*: http://www.bio-ontologies.org.uk/call-for-participa

CFP: for the Bio-Ontologies SIG at ISMB 2014

*Call for Participation for the Bio-Ontologies SIG at ISMB 2014* *What*: Bio-Ontologies SIG and Phenotype Day *When*: July 11 and July 12, 2014 *Where*: co-located with ISMB 2014 in Boston, MA ** Submissions Due: April 11th, 2014 (Fri) ** *More*: http://www.bio-ontologies.org.uk/call-for-participa

Bio-Ontologies SIG 2013 -- 10 days to submission deadline

st regards,* SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova

CFP - Bio-Ontologies SIG 2013, at ISMB/ECCB -- 31 days to submission deadline

st regards,* SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova

CFP - Bio-Ontologies SIG 2013, July 20, 2013, Berlin, Germany

* * *Best regards,* SIG Organizers: Nigam Shah, Susanna Sansone, Michel Dumontier, Larisa Soldatova

Call for participation in the Bio-Ontologies SIG 2013, July 20, 2013, Berlin, Germany

space and time will be allocated for a flash update on the poster. Flash updates are for short talks (5 min) giving the salient new developments on existing public ontologies. Unsuccessful papers will automatically be considered for poster presentation.* * * *Best regards,* SIG Organizers:

Medicine X Call for Papers

Dear Colleagues, I am forwarding a message about a meeting on Stanford campus, which may be of interest to those interested in the emerging area of social technologies and their effects on the field of medicine. IMIA's Social Media Working Group (SMWG) is handling the peer-review for this meeting.

17 days to submission deadline for Bio-Ontologies SIG 2012

*What*: Call for participation in the Bio-Ontologies SIG 2012 *Where*: July 13 - 14, 2012, Long Beach, CA. (Co-located with ISMB 2012) *When*: Submissions Due: April 13th, 2012 (Fri) *URL*: www.bio-ontologies.org.uk Dear Colleagues, The Bio-Ontologies SIG provides a forum for discussion of the la

Bio-Ontologies SIG 2012 -- 39 days to submission deadline

*What*: Call for participation in the Bio-Ontologies SIG 2012 *Where*: July 13 - 14, 2012, Long Beach, CA. (Co-located with ISMB 2012) *When*: Submissions Due: April 13th, 2012 (Fri) *URL*: www.bio-ontologies.org.uk Dear Colleagues, The Bio-Ontologies SIG provides a forum for discussion of the la

Bio-Ontologies SIG 2012 -- Call for participation

*What*: Call for participation in the Bio-Ontologies SIG 2012 *Where*: July 13 - 14, 2012, Long Beach, CA. (Co-located with ISMB 2012) *When*: Submissions Due: April 13th, 2012 (Fri) *URL*: www.bio-ontologies.org.uk Dear Colleagues, The Bio-Ontologies SIG provides a forum for discussion of the la

Summit on Translational Bioinformatics 2012 -- 3 days to panel, podium presentation, poster deadline

Dear Colleagues, The American Medical Informatics Association (AMIA) invites submissions for the 2012 Summit on Translational Bioinformatics (TBI), which will be held on March 19th-21st 2012 at the Parc 55 Hotel San Francisco, CA. The Summit is part of the Joint Summits on Translational Science an

Re: Socially Conscious Informatics

ctual tool? I could only find your > video presentation on the voting page. > Thanks! > http://facebook.com/mnkboulos > > > On Sun, Sep 18, 2011 at 7:23 PM, Nigam Shah wrote: > > Dear Friends@HCLS, > > Working with Grass Roots Science (http://grass-roots-scien

Socially Conscious Informatics

Dear Friends@HCLS, Working with Grass Roots Science (http://grass-roots-science.info/), we have created a tool for diabetics to prevent wound problems, and to help them cope if problems do happen. It requires only a very basic phone, no "internet literacy," and no "reading/writing" literacy to use

Invitation to participate in the Summit on Translational Bioinformatics 2012

Invitation to participate in the Summit on Translational Bioinformatics 2012 The American Medical Informatics Association (AMIA) invites submissions for the 2012 Summit on Translational Bioinformatics (TBI), which will be held on March 19th-21st 2012 at the Parc 55 Hotel San Francisco, CA. The Sum

CFP: Bio-Ontologies SIG 2011 - Submission deadline in 12 days

, M. et al. Integration and publication of heterogeneous text-mined relationships on the Semantic Web. Best regards, Nigam Shah (on behalf of the organizers)

CFP: Bio-Ontologies SIG 2011 - Submission deadline in 12 days.

, M. et al. Integration and publication of heterogeneous text-mined relationships on the Semantic Web. Best regards, Nigam Shah (on behalf of the organizers)

CFP: JBI Special Issue on Standards in Practice

*** Apologies for multiple postings *** * * *CALL FOR PAPERS* Journal of Biomedical Informatics Special Issue on Standards in Practice http://www.elsevier.com/locate/yjbin *Letter of Intent Due (optional): April 15, 2011* *Submission Deadline: August 1, 2011* *"Translating Standards into Practice

Bio-Ontologies SIG 2011 - Call for participation

new developments on existing public ontologies. Authors of posters can also indicate a desire to provide a flash update. Unsuccessful paper submissions will automatically be considered for poster presentation; there is no need to submit both on the same topic. Regards, Nigam Shah (on behalf of the organizers)

Bio-Ontologies SIG at ISMB/ECCB 2011 - Call for participation

new developments on existing public ontologies. Authors of posters can also indicate a desire to provide a flash update. Unsuccessful paper submissions will automatically be considered for poster presentation; there is no need to submit both on the same topic. Regards, Nigam Shah (on behalf of the organizers)

AMIA's 2011 Summit on Translational Bioinformatics -- Advance registration deadline is Feb 24th

will be held in the same venue (March 9-11). The joint summits will encompass biomedical informatics innovations across the full spectrum of translational science. We hope to see you in San Francisco! Regards, Nigam Shah

Summit on Translational Bioinformatics -- Early bird deadline Jan 27th.

full spectrum of translational science. We look forward to seeing you in San Francisco! On behalf of the SPC Members for AMIA-TBI, Nigam Shah

Deadline (Dec 15th) for poster and podium presentation at AMIA Summit on Translational Bioinformatics

Hotel San Francisco, where a block of rooms will be available for participants at a lower rate. Please visit http://jointsummits2011.amia.org/ for more information. We look forward to your participation in shaping this exciting Summit! Regards, Nigam Shah

2011 AMIA Summit on Translational Bioinformatics, Deadline for Abstract submissions, Dec 15th

Dear Colleagues, The deadline for abstract submissions (either for oral or poster presentations) to the 2011 AMIA Summit on Translational Bioinformatics is *December 15th*. As a new feature this year, the *top podium presentations will be invited for submission of full manuscripts to the Journal o

JBMS Special Issue on papers from Bio-Ontologies 2009 is out!

Dear all, On Behalf of the Bio-Ontology SIG organizers, I am pleased to inform you that the Journal of Biomedical Semantics supplement containing select papers from the Bio-Ontologies 2009 meeting is now available at: http://www.jbiomedsem.com/supplements/1/S1 Among the co-organizers, special cre

AMIA 2011 Summit on Translational Bioinformatics -- call for proposals

Dear Colleagues, I am delighted to share the call for proposals for the *AMIA 2011 Summit on Translational Bioinformatics, *March 7-9, 2011, ( http://jointsummits2011.amia.org/). Please share the details below with interested researchers at your institution. The American Medical Informatics Assoc

Re: ismb sig call for proposals is online

gt; >>> From: Hershel Safer > >>> Date: October 20, 2009 1:04:44 PM EDT > >>> To: Fran Lewitter , Rafi Najmanovich > >>> >>> >, Iddo Friedberg , Eduardo Eyras < > eduardo.ey...@upf.edu > >>> >, E Eyras , Hagit Shatkay , &g

Re: BioRDF Telcon

09, at 12:12 PM, Helen Parkinson wrote: > > Having the NIFSTD in bioportal would be ideal, we will always defer to NIF >> for neuroscience terms, >> >> best >> >> Helen >> >> Kei Cheung wrote: >> >>> Nigam Shah wrote: >>> >>&

Re: BioRDF Telcon

On Tue, Sep 1, 2009 at 6:37 AM, Helen Parkinson wrote: > The performance depends largely on how well the ontology is aligned with > the input data, for this reason we developed our own ontology. This is very true. However, if there is already an existing ontology that matches the input data wel

Re: Is there a benchmark of triple-stores with a "bias" to Life Sciences ?

> > However, I'm not aware of a review/benchmark of these systems, both >> regarding performances and features. >> I've seen a few links like: >> >> http://esw.w3.org/topic/LargeTripleStores >> >> or >> >> >> http://www4.wiwiss.fu-berlin.de/bizer/BerlinSPARQLBenchmark/results/index.html >> >> But I

RE: 'Gene WIki' announced

Hi Kei, Wikis are certainly gaining ground. If there are ways in which NCBO can contribute ontology services to such projects, we would be very happy to help. We can start simple by promoting the use of ontology term URIs provided by BioPortal (see Mark's message from earlier today [8/21]). If m

RE: 'Gene WIki' announced

Hi Kei, What I find odd is that the page http://dbpedia.org/page/Cerebrum, has a property ispartof, but on the query page (http://dbpedia.org/snorql/) if I run: SELECT ?brainregion WHERE { ?brainregion dbpedia2:ispartof } // NOTE: PREFIX db

Job Announcement at NCBO

Please forward this message to people who you believe might be interested. We would really love to get someone aware of HCLS activities for this position. Thanks, Nigam. Outreach Coordinator/Curator Job ID 30683 Job Location School of Medicine Job Category Research Salary 3P3 Date Posted

RE: [COI] CT#8 Drug Information Needed for Test Case Query

For the demonstration purpose, we can construct a small "drug" ontology to cover the above concepts and drug names. But the ideal way is to use an existing and well developed drug ontology for this purpose. Does anyone on the list know such ontology? Samson Tu at Stanford has built such a

RE: SenseLab note: some updates

>There is an interesting trade-off between post-coordinated and pre- >coordinated >vocabularies in the clinical context. > >For instance if you have the following concept fracture (site = femur, >laterality = left) this can be used in two contexts: >- In a search and exploration context, where pos

National Center for Biomedical Ontology - alpha release of Bioportal

any questions or need more information about the prototype, please feel free to email Nick Griffith at [EMAIL PROTECTED] Best Regards, Nigam Shah - Nigam Shah Research Scientist, Stanford Medical Informatics. Ph: 650.725.6236 Web: www.stanford.edu/~nigam/ -

RE: BioRDF Brainstorming

We (NCBO) can provide data tagged with UMLS CUIs. We don't have a URI service for CUIs yet, but once bioportal in URI-fitted (by sometime in march) we could have that. Nigam. From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of eric neumann Sent: Monday, February 11, 2008 7:17 AM

RE: One ontology schema - heterogeneous instance bases

Hi Satya, See below... >For example, the BioPAX ontology is a community effort to standardize >the representation of pathway data. But, there are serious differences >in the way concepts and relationships, defined in the BioPAX ontology >schema, are interpreted to create instances. This leads to

RE: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

>Fantastic material Nigam (and co)! I hope you don't mind if I use some >for my 4th year bioinformatics class :-) By all means... >Couple of points: > >Problem: Asserting disjointness between classes that are definable. >Example (slide 100): Rural Area and Urban Area are disjoint; Woomera is >i

RE: HCLS Demo at ISMB/ECCB, How to contribute to the demo?

>Matthias Samwald wrote: >... but the result is much >more useful when some basic ontology design criteria are met and the >information in the source databases is re-interpreted to form a >meaningful ontology. Unfortunately I cannot point you to a short, >comprehensive document that would describ

RE: [BioPAX-discuss] ISMB 2007 / Meeting of Semantic Web - interested people

Did the meeting (1) happen? -Nigam. >-Original Message- >From: [EMAIL PROTECTED] [mailto:biopax-discuss- >[EMAIL PROTECTED] On Behalf Of Matthias Samwald >Sent: Saturday, July 21, 2007 2:47 AM >To: public-semweb-lifesci; [EMAIL PROTECTED] >Cc: [EMAIL PROTECTED]; Eric Neumann; [EMAIL PRO

RE: Advancing translational research with the Semantic Web

Interesting thread. From the user perspective we still need a way to create these kinds of annotations (either on the statements/triples or on the model/graph). Rolling one's own reification mechanism or using named graphs (which don’t have support in RDF) is a technical decision point, but what a

RE: Notes from informal Demo F2F

Hi Alan, Tim and Steve (the other HyBrow guy) have discussed this in some detail I believe. Its great to have formally structured representations at the level of biological entities created by the scientists themselves. However, right now (A) The ontologies and relations for doing so might or mig

RE: Spatial queries against GENSAT or ABA

I did pass some emails around to the SMART Atlas folks early last week in order to get their feedback on Alan's work on the Google Maps Javascript API and backend PERL code to support caching images. The Google Maps API is one that has come up endless in these atlasing discussions, and it's nice to

RE: cell types, brain regions mentioned in gensat

> BTW, if someone has a theory of what the other number in > ontology.xls are, I'm all ears. Okay, pure guesses: Line 4 = Cerebral cortex,CTX,CH,176,255,184,3,85,4141526,61.647,29.999,33.711 176,255,184 seem like RGB values (they all range from 2 to 255) for that region in the image. 3 is a ser

Race/Ethnicity population descriptors

Hi Everyone, I am trying to find a comprehensive terminology/term-list for race/ethnicity and population descriptions. For example, dbSNP has a "population type" which is different from what Hapmap uses. I am looking for something beyond the usual, white/african/pacific islander etc that come on

RE: BioRDF [Telcon]

Hi June, ... Comments in line ... > In answer to Vipul's question about posting hypotheses and > querying the SWAN knowledge base, we are planning to manually > curate hypotheses. Each major hypothesis will be broken down > into claims, or scientific assertions, and linked to > supportive eviden

Parkinson's KB by Amarnath Gupta

http://portal.acm.org/citation.cfm?id=965624 Pdf: www.bioontology.org/wiki/images/7/75/Gupta_disease_ontology.pdf Above is the work on Parkinson's disease by Amarnath Gupta, which was mentioned (as a source of structured data for Parkinsons) at the HCLSIG workshop at ISWC. --Nigam.

RE: using OBO in owl format to describe data

> I am not familiar with the OBO, from what I just read from the > OBO spec, I think OBO does have term like "intersection_of", > "union_of", "disjoint_from". From I can see now, the > translation should be syntactic for most, but not all, > concepts. For those concepts that there is any OWL equiv

RE: demo for semantic publishing tool

Hi AJ,   this looks like a very light semantic on top of wordpress. Very similar to the Semantic Wiki project, where there is a semantic layer on top of mediawiki.   http://en.wikipedia.org/wiki/Semantic_MediaWiki   the advantage of semantic mediawiki is that the "ontology" used by people eme

RE: Size estimates of current LS space (and Introductions)

Hi June, Thanks for the detailed response. One follow up comment (not for you) below: > Could the scientific community perform this > vetting and editing function itself, a la wikipedia? We have > found that in general, this does not work. Many scientists > refuse to correct or criticize colleag

RE: Size estimates of current LS space (and Introductions)

Hi Jeremy, Please see inline comments below.. > The semantic web interests me for several reasons. For one, I > believe it will be a solid substrate for distributed curation, > which is a necessary part of the ongoing effort to improve the > quality of the biological data we use. > Like wikiped

RE: Ontology entity IDs

As I've mentioned earlier, I'm more comfortable with the sort of URI Alan presents below, than one where term strings are used as IDs.  In essence, the string 'GO' becomes a namespace ID, even if XML namespaces are not being explicitly involved here.    This 'GO' namespace would have three d

Computational Systems Bioinformatics Conference, August 14-18, 2006

[Apologies if you get this multiple times...] You are invited to submit posters to the 2006 Life Sciences Society Computational Systems Bioinformatics Conference (CSB2006). The conference's goal is to facilitate exchange of ideas and collaborations between computer scientists and biologis

Extending BioDash

ons' easily but cant find an easy way to add to it. The Add new item menu only allows adding of new collections, lists and to-do items. How to add a relation? Please point to any pointers, links to tutorials etc that can be useful here. --Nigam. - Nigam Shah