https://www.bioontology.org//mediawiki/api.php?action=feedcontributions&user=Googlefans&feedformat=atomNCBO Wiki - User contributions [en]2024-03-28T11:53:04ZUser contributionsMediaWiki 1.35.9https://www.bioontology.org//mediawiki/index.php?title=PATO_Meeting&diff=3771PATO Meeting2006-08-08T00:14:51Z<p>Googlefans: </p>
<hr />
<div>== General Information == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day meeting focused on the [http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_value Phenotype and Trait Ontology (PATO)] December 1-2, 2006 at Stanford University in Palo Alto, CA.<br />
<br />
[http://www.fruitfly.org/pato/pato-form.html Register here.][http://www.wow-gold-sell.com/ wow gold]<br />
<br />
==Draft agenda==<br />
<br />
*Thursday, November 30, 2006<br />
** 7pm: Informal gathering for dinner (Gordon Biersch?)<br />
<br />
*Friday, December 1, 2006<br />
**8:30 - 5:30pm Meeting<br />
***Introduction to PaTO<br />
***Phenote<br />
<br />
*Saturday, December 2, 2006<br />
**8:30 - 5:30pm Meeting<br />
<br />
==Venue ==<br />
[http://www.stanford.edu/home/welcome/campus/clark.html Stanford University Clark Center, room S360]<br />
<br />
[http://med.stanford.edu/maps/ Directions to Stanford Medical Center]<br />
<br />
[http://med.stanford.edu/maps/sumc.html Map of Stanford Medical Center]--see "C", Clark Center<br />
<br />
[http://transportation.stanford.edu/marguerite/MargueriteSched.shtml Directions on taking Free Marguerite Shuttle Bus]--take Line A to Medical Center<br />
<br />
==Accommodations==<br />
<br />
We aren't reserving a block of rooms anywhere, but these local hotels are close by and have Stanford shuttle service.<br />
<br />
*[http://www.hotelcalifornia.com/ Hotel California]<br />
*[http://www.cardinalhotel.com/ Cardinal Hotel]<br />
*[http://woodsidehotels.com/stanford/index.html Stanford Park Hotel]<br />
*[http://www.starwoodhotels.com/sheraton/property/overview/index.html?propertyID=214 Sheraton]<br />
<br />
==Talk List==<br />
<br />
Russ Altman: Challenges for Representing Phenotype in Pharmacogenomics <br /><br />
*Abstract: The PharmGKB (http://www.pharmgkb.org/) is an online resource devoted to comprehensive cataloguing of genetic variations relevant to variation in drug response. We curate primary data (genotype, phenotype at molecular, cellular, clinical level) as well as knowledge (literature curation, pathways, human annotations of key genes). We provide search and visualization tools for this information, in order to catalyze research in pharmacogenomics. For both activities, we need to index the relevant phenotypes for the purposes of indexing, aggregation, search, and automatic summarization and data mining. We need a flexible method for annotating phenotypes that are described in the literature (by curators). We would prefer to adopt community-based standards that would allow PharmGKB to interoperate with other databases, both human and model organism.</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Shared_Materials&diff=3770Shared Materials2006-08-08T00:14:42Z<p>Googlefans: </p>
<hr />
<div>This page lists materials shared among members of cBiO<br />
<br />
==cBiO Documents==<br />
[[Media:cbio-r01-plan.v11.doc|Collaboration Plan]]<br />
<br />
[[Media:cBiO-5-pg Center Overview.v3.doc|Center Overview 5-page document]]<br />
<br />
[[Media:cbio_flyer_v3.pdf|cBiO Brochure]]<br />
<br />
[[Media:OBO-Foundry.doc|OBO Foundry]]<br />
<br />
==cBiO Policies and Guidelines==<br />
[[Citing the Center]]<br />
<br />
[[Acknowledgements in cBiO Papers]]<br />
<br />
==PowerPoint Presentations==<br />
<br />
===Project meeting March 2006 Talks===<br />
<br />
*[[Media:OBO-Core-Criteria.ppt|OBO Core Criteria, Barry Smith slides]]<br />
*[[Media:AHM_Ashburner.ppt|Cambridge: Ashburner]]<br />
*[[Media:AHM_Barry.ppt|Buffalo: Smith]]<br />
*[[Media:AHM_Core1.ppt|Stanford: Murphy]]<br />
*[[Media:AHM_LexGrid.ppt|Mayo: Buntrock]]<br />
*[[Media:AHM_Monte.ppt|UOregon: Westerfield]]<br />
*[[Media:AHM_Sim.ppt|UCSF: Sim]]<br />
*[[Media:AHM_Peggy.ppt|UVic: Storey]]<br />
*[[Media:AHM_Suzi.ppt|Berkeley: Lewis]]<br />
*[[Media:AHM_OBD.ppt|Berkeley: Mungall]]<br />
<br />
===AMIA 2005 Talks===<br />
#[[Media:Musen AMIA Panel.ppt|Mark Musen slides]]<br />
#[[Media:AMIA_Bioontology_05.pdf|Chris Chute slides]]<br />
#[[Media:SmithpanelSemantics.ppt|Barry Smith slides]]<br />
#[[Media:AMIA_Oct2005_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===CSH Talks===<br />
#[[Media:CSHL_22Oct2005_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===NCOR Talks===<br />
#[[Media:cBio-NCOR_SLewis.ppt|Suzi Lewis slides]]<br />
<br />
===Phenotype November 2005 Talks===<br />
#[[Media:Westerfield_Pheno_CSH.ppt|Monte Westerfield slides]]<br />
#[[Media:Drysdale_Pheno_CSH.ppt|Rachel Drysdale slides]]<br />
#[[Media:Mungall_Pheno_CSH.ppt|Chris Mungall slides]]<br />
<br />
===Phenotype December 2005 Talks===<br />
* [[Media:cBioMockup_ZFIN0512.pdf|Erik Segerdell mockup]]<br />
* [[Media:cBioRequirements_ZFIN0512.doc|Melissa Haendel and Erik Segerdell requirements]]<br />
* [[Media:Uvic_viztools_Asimilar_Dec2005.ppt|Peggy Storey's (UVic) presentation on visualization]]<br />
<br />
===NIH Kickoff Meeting Talks Dec 2005===<br />
* [[Media:cBiO NCBC kickoff mtg.ppt|Kickoff Meeting Slides]]<br />
<br />
===HCLS===<br />
* [[Media:Musen W3C HCLS-converted.ppt|HCLS meeting]]<br />
<br />
===Ontology Talks===<br />
* [[Media:OntologyJoy.ppt|Suzi SMI Talk]][http://www.wow-gold-sell.com/ wow gold]<br />
<br />
===PATO meeting May 2006, Hinxton===<br />
*[[Media:Phenote-pato-hinxton-may-2006.ppt|Phenote slides, Mark Gibson]]<br />
<br />
===Berkeley-Stanford July 10 meeting===<br />
*[[Media:Phenote-stanford-july-2006.ppt|Phenote slides,Mark Gibson]]</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Workshop_on_Ontology_of_Diseases&diff=3769Workshop on Ontology of Diseases2006-08-08T00:14:29Z<p>Googlefans: </p>
<hr />
<div>== General Information == <br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of diseases on November 6-7, 2006 in Baltimore, MD.<br />
<br />
The goals of the workshop are to promote sound, principles-based ontology construction and to raise the level of cooperation between people who work in this and related fields.<br />
<br />
== Participation ==<br />
<br />
'''PLEASE NOTE THAT REGISTRATION IS CLOSED.'''<br />
<br />
If you have any suggestions or questions about the workshop, please don't hesitate to contact [[User:Neuhaus| Fabian Neuhaus]][http://www.wow-gold-sell.com/ wow gold].<br />
<br />
== Preliminary Agenda ==<br />
<br />
'''Monday November 6'''<br />
<br />
''Morning''<br />
<br />
- Introduction<br />
<br />
- Session I: Disease Ontologies - Where We Are<br />
(Moderator: Rex Chisholm)<br />
* Rex Chisholm: OBO Disease Ontology <br />
* Winston Hide or Oliver Hofmann: eVOC Ontologies <br />
* Kent Spackman: SNOMED CT<br />
<br />
<br />
''Afternoon'' <br />
<br />
- Session II: What is a Disease?<br />
(Moderator: Barry Smith)<br />
<br />
<br />
'''Tuesday November 7'''<br />
<br />
''Morning''<br />
<br />
- Session III: Problems of Disease Ontologies<br />
(Moderator: Werner Ceusters)<br />
<br />
<br />
''Afternoon'' <br />
<br />
- Session IV: The Next Steps: Moderated Discussion (Moderatrix: Suzanna Lewis)<br />
<br />
- Informal Strategy Session<br />
<br />
<br />
(The workshop will start on Monday November 6 at 9 am and will end on Tuesday November 7 at 6 pm.)<br />
<br />
<br />
<br />
== Participants ==<br />
<br />
Carol Bean -– National Center for Research Resources, National Institutes of Health, U.S.A <br />
<br />
Olivier Bodenreider -– National Library of Medicine, U.S.A <br />
<br />
Mathias Brochhausen -– IFOMIS, Saarland University, Germany <br />
<br />
Werner Ceusters -– ECOR, Saarland University, Germany <br />
<br />
Rex Chisholm -– Center for Genetic Medicine, Northwestern University, U.S.A <br />
<br />
Christopher Chute -– NCBO, Mayo Clinic College of Medicine, U.S.A <br />
<br />
Elaine Collier -– National Center for Research Resources, National Institutes of Health, U.S.A <br />
<br />
Lindsay Cowell -– Immunology, Duke University, U.S.A. <br />
<br />
Yong Gao -– Massachusetts General Hospital, Harvard Medical School, U.S.A<br />
<br />
Louis Goldberg -– Oral Biology, University at Buffalo, U.S.A <br />
<br />
Peter Good -– National Human Genome Research Institute, U.S.A<br />
<br />
Kristel Hackett -– MGH Laboratory of Computer Science, U.S.A <br />
<br />
Frank Hartel -– National Cancer Institute, National Institutes of Health, U.S.A <br />
<br />
Winston Hide -– SANBI, University of<br />
the Western Cape, South Africa <br />
<br />
Oliver Hofmann -– SANBI, University of<br />
the Western Cape, South Africa <br />
<br />
Ingvar Johansson -– IFOMIS, Saarland University, Germany <br />
<br />
Anand Kumar -– IFOMIS, Saarland University, Germany <br />
<br />
Dirk Lanzerath -– German Reference Centre for Ethics in the Life Sciences, Germany<br />
<br />
Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory, U.S.A<br />
<br />
Onard Mejino -– Structural Informatics Group, University of Washington, U.S.A<br />
<br />
Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory, U.S.A<br />
<br />
Fabian Neuhaus -– NCBO, University at Buffalo, U.S.A <br />
<br />
Richard Scheuermann -– Pathology, U.T. Southwestern Medical Center, U.S.A<br />
<br />
Stefan Schulz -– Medical Informatics, Freiburg University Hospital, Germany<br />
<br />
Kent Spackman -– Medical Informatics, Oregon Health & Science University, U.S.A <br />
<br />
Nigam Shah -– NCBO, Stanford Medical Informatics, U.S.A <br />
<br />
Barry Smith -– NCBO, University at Buffalo, U.S.A <br />
<br />
Lynn Schriml -– The Institute for Genomic Research, USA<br />
<br />
Monte Westerfield -– Institute of Neuroscience, University of Oregon, U.S.A<br />
<br />
Owen White -– The Institute for Genomic Research, U.S.A<br />
<br />
Neil Williams -– Philosophy, University at Buffalo, U.S.A<br />
<br />
==Venue ==<br />
Inn at the Colonnade<br />
4 West University Parkway<br />
Baltimore, Maryland 21218<br />
Telephone: +1 410 235 5400<br />
Fax: +1 410 235 5572<br />
<br />
The Inn at the Colonnade is located across from Johns Hopkins University<br />
less than four miles from Baltimore's CBD and historic Inner Harbor, and<br />
only 20 minutes from BWI International Airport.<br />
<br />
A block of rooms have been reserved for those Workshop participants and<br />
attendees wishing to stay at the Inn at the Colonnade. Reservations may<br />
be made by calling 1-800-222-TREE. When making reservations, workshop<br />
participants and attendees are asked to identify themselves as being a<br />
member of the NCBO group. All reservations must be guaranteed for late<br />
arrival by charging to a major credit card. Workshop participants and<br />
attendees are encouraged to make room reservations no later than<br />
10/15/06. After 10/15/06, the Inn at the Colonnade may offer unused<br />
rooms held in the NCBO block to other customers. Reservations requested <br />
by Workshop participants and attendees after 10/15/06 will be accepted <br />
by the Inn at the Colonnade based upon availability and prevailing rates.<br />
<br />
<br />
<br />
== Links and Literature ==<br />
The workshop is associated with [http://www.formalontology.org/fois-2006/FOIS-2006%20Call%20for%20Papers.htm/ FOIS 2006] and KRMed 2006. <br />
<br />
[http://diseaseontology.sourceforge.net/ OBO disease ontology]<br />
<br />
[http://www.evocontology.org/site/Main/BrowseEvoc eVOC ontologies]<br />
<br />
[http://www.snomed.org/ SNOMED]<br />
<br />
[http://www.physiome.org/Models/ Physiome Project]<br />
<br />
[http://www.biohealthbase.org/ Biohealthbase]<br />
<br />
<br />
Amarnath Gupta et alia: [[Media:gupta_disease_ontology.pdf| Towards a formalization of disease-specific ontologies for neuroinformatics]].<br />
<br />
Cornelius Rosse, Anand Kumar, Jose LV Mejino Jr, Daniel L Cook, Landon T Detwilern and Barry Smith, “[http://ontology.buffalo.edu/bio/OBR.pdf A Strategy for Improving and Integrating Biomedical Ontologies]”<br />
<br />
Barry Smith, Werner Ceusters, Anand Kumar and Cornelius Rosse, “[http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf On Carcinomas and Other Pathological Entities]”, Comparative and Functional Genomics<br />
<br />
Some papers on [http://ontology.buffalo.edu/medo/SNOMED_Smith.html SNOMED].</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=BioPortal_FAQ&diff=3768BioPortal FAQ2006-08-08T00:12:17Z<p>Googlefans: </p>
<hr />
<div>Frequently Asked Questions within cBio<br />
<br />
This FAQ is currently in alpha - please be patient...<br />
<br />
=General=<br />
<br />
==NCBO==<br />
<br />
===What is NCBO?===<br />
<br />
National Center for Biomedical Ontology<br />
<br />
==OBO==<br />
<br />
===What is OBO?===<br />
<br />
Open Biomedical Ontologies<br />
<br />
===Where are the ontologies?===<br />
<br />
Currently on http://obo.sourceforge.net<br />
<br />
Soon to be moving to the NCBO site<br />
<br />
===How do I submit an ontology?===<br />
<br />
The current protocol is:<br />
<br />
Send an email to the obo-discuss mailing list, even if the ontology is in planning stages<br />
<br />
If the ontology satisfies basic criteria, we will add it to the OBO metadata and it will appear on the OBO site<br />
<br />
Soon we will have an ontology submission service on the NCBO website<br />
<br />
=Ontology Content=<br />
<br />
==Building Ontologies==<br />
<br />
===How do I go about building an ontology?===<br />
<br />
===What is the OBO Foundry?===<br />
<br />
A collaborative experiment, involving a group of ontology developers who have agreed in advance to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies within the broader OBO framework, and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.<br />
<br />
===Where is the OBO Foundry?===<br />
<br />
See http://obofoundry.org/ [http://www.wow-gold-sell.com/ wow gold]<br />
<br />
==Current Ontologies==<br />
<br />
===incomplete is-a paths===<br />
<br />
Many OBO ontologies are currently incomplete with respect to all classes/terms having an is-a parent. Many tools (including OBO-Edit and AmiGO) deliberately allow the conflation of relations when presenting the ontology as a DAG or a tree to the user. However, other tools (including Protege and SWOOP) do not. This means that some OBO ontologies can look unusual when viewed with these other tools (lots of classes appear at the root level).<br />
<br />
This is currently being addressed by the maintainers of OBO ontologies. An effort is underway to complete the is-a parentage in the GO cellular component ontology (biological process will be more difficult). The Plant Ontology Consortium are completing the is-a parentage in the plant anatomical structure ontology.<br />
<br />
Until this work is complete, some OBO ontologies may look unusual when viewed in conventional ontology browsing and editing tools. With some of these tools, there may be some configurations which allow other relations to be conflated with the is-a relation when presenting the ontology as a DAG or tree view.<br />
<br />
One option is to automatically create an is-a parent to the ontology root for every non-root class/term which lacks any is-a parents. Note that this may create inconsistencies in the ontology if the genuine is-a parent is somewhere deeper in the ontology hierarchy; nevertheless this step may be necessary before presenting some OBO ontologies to tools such as reasoners.<br />
<br />
=Technical=<br />
<br />
Questions for cores 1 and 2<br />
<br />
==OBO Format==<br />
<br />
Questions about the OBO text and xml formats<br />
<br />
===What is OBO Format?===<br />
<br />
===Is OBO Format different from the old GO format?===<br />
<br />
Yes. The old dag-edit format (i.e. the one in which indentation was used to denote the GO hierarchy) is STRONGLY deprecated.<br />
<br />
===Where can I find the spec?===<br />
<br />
You can find details on the 1.0 spec on the GO home page<br />
http://www.geneontology.org/GO.format.shtml#oboflat<br />
<br />
This spec is somewhat underspecified<br />
<br />
The 1.2 spec is in preparation, and will be released to coincide with the first production OBO-Edit release sometime early in 2006<br />
<br />
You can find a preliminary version of the spec here:<br />
HTML -- http://www.godatabase.org/dev/doc/obo_format_spec.html<br />
PDF -- http://www.godatabase.org/dev/doc/obo_format_spec.pdf<br />
Ascii text -- http://www.godatabase.org/dev/doc/obo_format_spec.txt<br />
<br />
===Why not use XML?===<br />
<br />
There is also an obo-xml format. See<br />
<br />
http://www.godatabase.org/dev/xml<br />
<br />
Currently only available as DTD. Relax-NG and XSD coming soon.<br />
<br />
===Is there a UML model?===<br />
<br />
Yes, there is a UML translation of the obo format in progress, produced by Harold Solbrig of Mayo clinic; see:<br />
<br />
http://informatics.mayo.edu/schema/OBO/UMLModel/HTML/<br />
<br />
===What tools support Obo-Format?===<br />
<br />
The following are *ontology* tools that support the OBO format. There are many other tools for the analysis of gene ontology data which also happen to read the OBO format - see http://www.geneontology.org/GO.tools.shtml for a list<br />
<br />
; OBO-Edit<br />
: (naturally!). You should use this rather than DAG-Edit (DAG-Edit still supports obo-1.0 format), as DAG-Edit is deprecated as of 2006.<br />
<br />
; COBRA<br />
: developed by Stuart Aitken as part of http://www.xspan.org. COBRA is a java ontology editor/viewer for aligning ontologies<br />
<br />
; go-perl<br />
: http://search.cpan.org/~cmungall/go-perl<br />
<br />
==Using Protege with OBO ontologies==<br />
<br />
You have two options here - use the Protege OBO plugin, or convert to a format which Protege understands.<br />
<br />
The OBO plugin was developed at the University of Washington, and is no longer supported.<br />
<br />
You can convert any obo-format file to OWL and use Protege-OWL (but not Protege-classic); see the next entry.<br />
<br />
Note that when you look at many of the OBO ontologies in Protege (classic or Protege-OWL) you will see that there are large amounts of classes apparently at the root level. This is because OBO ontologies have historically not been complete with respect to all classes having a superclass (is-a parent). This is currently being addressed. See the FAQ entry on this subject.<br />
<br />
===Can I convert Obo-format to OWL?===<br />
<br />
Yes. At this present time, the best way of foing this is to use the xslts included in go-perl.<br />
Download and install:<br />
http://search.cpan.org/~cmungall/go-perl/<br />
Then run the script<br />
<br />
go2owl myontology.obo<br />
<br />
This functionality will soon be available from oboedit<br />
<br />
For more details on the mapping, see:<br />
<br />
http://www.fruitfly.org/~cjm/obol/doc/mapping-obo-to-owl.html<br />
<br />
===OK, but can I just download OBO ontologies as OWL without doing the conversion myself?===<br />
<br />
You can, at least for some OBO ontologies. This is an experimental service, and will eventually be subsumed into the services provided by cBio:<br />
<br />
http://www.fruitfly.org/~cjm/obo-download<br />
<br />
===Can I convert Obo-format files to Protege-classic?===<br />
<br />
Not yet. In theory it should not be hard to provide an XSL for this. The reverse transformation may be more difficult.<br />
<br />
==Ontology Metadata==<br />
<br />
==OBD==<br />
<br />
===What is OBD?===<br />
<br />
OBD is a database for storing data typed using OBO ontologies<br />
<br />
===Where is it?===<br />
<br />
In development!<br />
<br />
===Is there a demo?===<br />
<br />
See http://www.fruitfly.org/~cjm/obd<br />
<br />
===Datasets===<br />
<br />
See the above URL for now</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Phenotype_Reading_List&diff=3767Phenotype Reading List2006-08-08T00:12:06Z<p>Googlefans: </p>
<hr />
<div>=Phenotype readling list=<br />
<br />
I have some of these in my endnote library, but endnote is terrible<br />
for collecting non-bio references. I'm guessing the CS and logiv<br />
people use Latex? If so, if they post their bibtexes here I can<br />
compile both an endnote and a bibtex library.<br />
<br />
==Intro to phenotypes for non-biologists==<br />
<br />
This list is very fly-centric. If someone can contribute zebrafish and<br />
human clinical genetics pointers that would be great. <br />
<br />
===Genetics of Development===<br />
<br />
Only looked briefly at this, but seems like it might be a useful non-biologists intro. Nice images.<br />
<br />
http://www.learner.org/channel/courses/biology/units/gendev/<br />
<br />
===EBI Introduction to cell biology===<br />
<br />
This is microarray centric (we'll need to turn our attention to this technology at some point), but still v useful for the non-biologist<br />
<br />
http://www.ebi.ac.uk/microarray/biology_intro.html<br />
<br />
===Drysdale R: Phenotypic data in FlyBase=== <br />
Brief Bioinform 2001,2(1):68-80.<br />
<br />
This is an ideal intro for folks familiar with biological databases<br />
looking to make the first step into genetics and phenotypes.<br />
<br />
===Essential Developmental Biology===<br />
by J. M. W. Slack<br />
<br />
http://books.google.com/books?ie=UTF-8&hl=en&id=BXfdbKLTiZQC&dq=essential+developmental+biology&prev=http://books.google.com/books%3Flr%3D%26client%3Dfirefox-a%26q%3Dessential%2Bdevelopmental%2Bbiology&lpg=PP5&pg=PP5&printsec=4&sig=FIivE3wd7u_AC9ojAEdW-BpD90A [http://www.wow-gold-sell.com/ wow gold]<br />
<br />
I found this to be a really useful and accessible introduction to<br />
developmental biology. Remember, many of the phenotypes we're dealing<br />
with will be developmental. It may be challenging for those with<br />
virtually no biology, but I'd still highly recommend it. Covers fly,<br />
zebrafish and other major model organisms.<br />
<br />
===Other books===<br />
<br />
These two are standard texts for molecular biology - this will have a lot of the background material for understanding phenotypes:<br />
<br />
Alberts, B. , Bray, D. , Lewis J. , Raff, M., Roberts, K., Watson, J.D.: Molecular biology of the cell. New York, Garland Publishing, 1994<br />
<br />
Lewin B: Genes VII, New York, Oxford University Press, 2000<br />
<br />
This may also be useful:<br />
<br />
The Shape of Life : Genes, Development, and the Evolution of Animal Form (Paperback)<br />
by Rudolf A. Raff<br />
<br />
<br />
===THE ART AND DESIGN OF GENETIC SCREENS===<br />
<br />
This is actually a whole collection of reviews in Nature Reviews<br />
Genetics coverisg zebrafish, mouse, etc. Go to their website and<br />
search on the above:<br />
<br />
http://search.nature.com/search/?sp_a=sp1001702d&sp_sfvl_field=subject%7Cujournal&sp_t=results&sp_q_1=Nature+Reviews+Genetics&sp_x_1=ujournal&sp_p_1=phrase&go.x=0&go.y=0&sp-q=the+art+and+design+of+genetic+screens<br />
<br />
Here's the one on zebrafish<br />
http://www.nature.com/nrg/journal/v2/n12/abs/nrg1201-956a_fs.html;jsessionid=C33F00DB1D1DF6C5E26BCD324FFE25B4<br />
<br />
These are highly recommended for the tools developers<br />
<br />
===The Making of a Fly: The Genetics of Animal Design [BOOK]===<br />
<br />
http://www.amazon.com/gp/product/0632030488/103-3091658-4208606?v=glance&n=283155<br />
<br />
May be hard going for those without any knowledge of genetics<br />
<br />
===Drosophila: A Laboratory Handbook, Michael Ashburner [BOOK]===<br />
aka the grey book<br />
http://www.cshlpress.com/default.tpl?action=full&cart=1133810703113928&--eqskudatarq=467&newtitle=Drosophila%3A%20A%20Laboratory%20Handbook%2C%20Second%20Edition<br />
<br />
Everything you ever wanted to know about Drosophila genetics but were<br />
afraid to ask Michael. This may be a little overwhelming for the CS<br />
folks<br />
<br />
==Formal ontology and logic==<br />
<br />
References on formal ontology and logic and qualities that are tied to<br />
qualities<br />
<br />
===A formal theory of substances, qualities, and universals.===<br />
<br />
Neuhaus, F., Grenon, P., Smith, B.: In Varzi, A., Vieu, L., eds.:<br />
Formal Ontology in Information Systems (FOIS’04), Turin, Italy, IOS<br />
Press (2004) 49–59<br />
<br />
Available from: http://ontology.buffalo.edu/bfo/SQU.pdf<br />
<br />
This paper may be heavy-going for those without a background in logic,<br />
but I would still highly recommend the first couple of pages to<br />
everyone involved in this project.<br />
<br />
===Stanford Encyclopedia of Philosophy===<br />
<br />
Entry on properties: http://plato.stanford.edu/entries/properties/<br />
<br />
I think properties here are used in the sense that Fabian Neuhaus and<br />
I would use "quality", rather than in the looser sense that a CS or<br />
OWL person may use the term.<br />
<br />
Entry on determinate vs determinable: http://plato.stanford.edu/entries/determinate-determinables/<br />
<br />
I was hesitant about adding this one. Inquiring minds may want to<br />
check this out. Determinate vs determinable roughly corresponds to<br />
value vs attribute<br />
<br />
==Data modeling==<br />
<br />
===J. Diederich. Basic properties for biological databases: character development and support===<br />
in Math. Comput. Modelling 25 (1997), 109-127.<br />
<br />
Required reading for everyone in the project. 1997, but it anticipated<br />
many of the problems we are facing. This has more of a systematics<br />
focus, but really the design of ontologies for phenotypic characters<br />
should be independent of whether we are applying this to genetic<br />
screens or to phylogenetic classisification.<br />
<br />
==See also an application of the work from this paper in:<br />
Diederich, J., R. Fortuner and J. Milton. 1997. Construction and integration<br />
of large character sets for nematode morpho-anatomical data. ''Fundam. appl. Nematol.'' 20: 409-424<br />
<br />
===Papers by George===<br />
<br />
George gets his own section here. The GB is paper is a good<br />
introduction to the EAV model as it was originally formulated in 2003.<br />
<br />
<br />
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Building<br />
mouse phenotype ontologies. Pac Symp Biocomput 2004:178-189.3.<br />
http://helix-web.stanford.edu/psb04/gkoutos.pdf<br />
<br />
Gkoutos GV, Green EC, Mallon AM, Hancock JM, Davidson D: Using<br />
ontologies to describe mouse phenotypes. Genome Biol 2005, 6(1):R8.4.<br />
http://dx.doi.org/10.1186/gb-2004-6-1-r8<br />
<br />
G. V. Gkoutos, E. C. J. Green, A.-M. Mallon, A. Blake, S. Greenaway 1, J. M. Hancock, D. Davidson<br />
Ontologies for the description of mouse phenotypes<br />
MRC Mammalian Genetics Unit, Harwell, UK<br />
http://doi.wiley.com/10.1002/cfg.430<br />
<br />
Gkoutos GV, Green EC, Greenaway S, Blake A, Mallon AM, Hancock JM:<br />
CRAVE: a database, middleware and visualization system for phenotype<br />
ontologies. Bioinformatics 2005, 21(7):1257-1262.<br />
http://www.bioinformatics.oupjournals.org/cgi/doi/10.1093/bioinformatics/bti147<br />
<br />
<br />
[[User:Cjm|Cjm]] 12:03, 5 December 2005 (PST)</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Workshop_on_Clinical_Trial_Ontology&diff=3766Workshop on Clinical Trial Ontology2006-08-08T00:11:30Z<p>Googlefans: </p>
<hr />
<div>== General Information ==<br />
<br />
The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Clinical Trials. The workshop will take place in May 2007 at a venue to be determined.<br />
<br />
== Aim of the workshop ==<br />
<br />
The aim of the workshop is to foster the creation of a reference ontology (high-quality controlled structured vocabulary) for clinical trial annotation. The ontology should comprehend terms like: ''cohort, randomization, placebo, response, efficacy, control, protocol, null hypothesis, control, confidence interval, finding, biomarker,'' etc., including also major relevant statistical terms and terms drawn from the CDISC [http://www.cdisc.org/glossary/clinicalterminologyv4.pdf glossary.]The ontology will organize these terms in a structured way, providing definitions and logical relations designed to advance reasoning with the data annotated in its terms.<br />
<br />
The proposed CTO should:<br />
<br />
(1) fully and faithfully capture the types of entities and relationships involved in clinical trials of any experimental design<br />
<br />
(2) comprehend all the terms needed for the task of meta-analysis of clinical trials<br />
<br />
(3) support trial bank interoperation<br />
<br />
(4) form an integral part of a more comprehensive investigation ontology, including also the [http://fugo.sourceforge.net/ Functional Genomics Investigation Ontology], which should form part of the [http://obofoundry.org/ OBO Foundry].<br />
<br />
The purpose of the meeting is to bring together representatives of the major groups involved in clinical trial informatics, design, execution, analysis and standardization in order to approve an initial draft of the CTO and create a strategy for its further development and testing. <br />
<br />
Further topics to be addressed include:<br />
<br />
i. The relation between CTO and data-model-oriented initiatives (HL7, CDISC, BRIDG, caBIG).<br />
<br />
ii. The relation between CTO and a drug (trial) ontology <br />
<br />
iii. The relation between CTO and an epidemiology study ontology<br />
<br />
iv. The proper treatment of ''types'' (surgical intervention, tumor, human being) and ''instances'' (Jane's oophorectomy, John's tumor, Fritz) in ontologies and related artifacts.<br />
<br />
v. The relation between CTO, Trialbank, and OBD.<br />
<br />
== Agenda ==<br />
<br />
== Participation ==<br />
<br />
'''PLEASE NOTE THAT PARTICIPATION IN THIS MEETING IS RESTRICTED.''' <br />
<br />
If you wish to be considered for participation, please send a brief statement to [mailto:phismith@buffalo.edu Barry Smith][http://www.wow-gold-sell.com/ wow gold].<br />
<br />
== Participants (Initial List) ==<br />
<br />
Carol Bean -- NIH/NCRR<br />
<br />
Werner Ceusters -- NCBO, University at Buffalo<br />
<br />
Chris Chute -- NCBO, Mayo Clinic, Rochester, MN<br />
<br />
Lindsay Cowell -- Duke University<br />
<br />
Liju Fan -- Ontology Workshop, LLC<br />
<br />
Jennifer Fostel -- NIH/NIEHS<br />
<br />
Gilberto Fragoso -- NIH/NCI<br />
<br />
Louis J. Goldberg -- University at Buffalo<br />
<br />
Federico Goodsaid -- (FDA CDER, Office of Clinical Pharmacology)<br />
<br />
Norbert Graf -- [http://acgt.ercim.org/ ACGT], Homburg, Germany<br />
<br />
Ted Grasela -- Cognigen Corporation, Amherst, NY<br />
<br />
Tina Hernandez-Boussard -- PharmGKB, Stanford University<br />
<br />
Suzanna Lewis -- NCBO, Berkeley<br />
<br />
Chris Mungall -- Howard Hughes Institute<br />
<br />
Mark Musen -- NCBO, Stanford University<br />
<br />
Fabian Neuhaus -– NCBO, University at Buffalo <br />
<br />
Philippe Rocca-Serra -- EBI, Hinxton, Cambridge<br />
<br />
Nigam Shah -– NCBO, Stanford Medical Informatics<br />
<br />
Susanna Sansone -- EBI, Hinxton, Cambridge<br />
<br />
Ida Sim -- NCBO, University of California at San Francisco Medical Center<br />
<br />
Barry Smith -– NCBO, University at Buffalo<br />
<br />
Holger Stenzhorn -- IFOMIS, Saarbrücken<br />
<br />
Weida Tong -- Center for Toxicoinformatics, FDA NCTR<br />
<br />
Samson Tu -- Stanford University<br />
<br />
Gabriele Weiler -- Fraunhofer Institute, Sankt Ingbert, Germany<br />
<br />
== Venue ==</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Anatomy_Ontology_Workshop&diff=3765Anatomy Ontology Workshop2006-08-08T00:11:18Z<p>Googlefans: </p>
<hr />
<div>== General Information ==<br />
<br />
The National Center for Biomedical Ontology will host a two-day workshop focused on the Ontology of Anatomy. The workshop will take place on September 8-9, 2006 in Seattle.<br />
<br />
== Participation ==<br />
<br />
'''PLEASE NOTE THAT REGISTRATION IS CLOSED.'''<br />
<br />
If you have any suggestions or questions about the workshop, please don't hesitate to contact [[User:Neuhaus| Fabian Neuhaus]].[http://www.wow-gold-sell.com/ wow gold]<br />
<br />
== Aim of the workshop == <br />
At the Workshop for the Ontology of Anatomy we want to gather researchers who are actively involved in the development and improvement of particular anatomy ontologies for a variety of organisms. Regardless of organism differences, if we use common methodologies and principles to build our ontologies then, ultimately, this will enable us to tackle the big issue: to recognize homologous anatomical structures of different species.<br />
<br />
The main focus of this workshop is to pave the way for interoperability between the anatomical ontologies developed for various organisms (including human) by agreeing on shared methodologies for building our respective ontologies. <br />
<br />
Its objectives are to develop:<br />
<br />
1. a list of relations (especially part_of) used within anatomical anatomies, including definitions and rules for consistent use within anatomy ontologies ;<br />
<br />
2. a list of major organizational units of biological organisms at all levels of granular partitions (e.g. biological macromolecule, cell, organ);<br />
<br />
3. a representation of developmental stages of organisms; are anatomy and development two separate or one single integrated ontology? If separate what are the relations between them and how should they be applied;<br />
<br />
4. a method that allows automated reasoners to recognize homologous anatomical structures of different species.<br />
<br />
== Agenda ==<br />
In order to meet our objectives, we need to create a common anatomy reference ontology (CARO) designed to ensure interoperability of the anatomy ontologies developed for specific organisms. This common ontology will comprehend both top-level categories and a common set of relations to be used within anatomical ontologies; CARO will be embedded in a set of principles for constructing anatomy ontologies for different organisms at different developmental stages. The discussion will be based on a pre-version of CARO.<br />
<br />
The workshop will consist of four sessions (not necessarily in this order):<br />
* The Range of CARO and its relation to species specific anatomies<br />
* Relations and development in CARO<br />
* The top level CARO universals<br />
* Concrete steps to implement CARO<br />
<br />
(The workshop will start on Friday September 8 at 9 am and will end on Saturday September 9 at 6 pm.)<br />
<br />
== Participants ==<br />
<br />
Stuart Aitken -– Artificial Intelligence Applications Institute, University of Edinburgh<br />
<br />
Michael Ashburner -– NCBO, University of Cambridge<br />
<br />
Carol Bean -– National Institutes of Health<br />
<br />
Thomas Bittner -– Philosopy, University at Buffalo<br />
<br />
Judith Blake -– The Jackson Laboratory<br />
<br />
Albert Burger -– Medical Research Council, Human Genetics Unit, Edinburgh<br />
<br />
Rex Chisholm -– Center for Genetic Medicine, Northwestern University<br />
<br />
Sherri De Coronado -– National Cancer Institute, Center for Bioinformatics <br />
<br />
Louis Goldberg -– Oral Biology, University at Buffalo<br />
<br />
Melissa Haendel -– Zebrafish Information Network, University of Oregon<br />
<br />
Marc Halfon -– Biochemistry, University at Buffalo<br />
<br />
Terry Hayamizu -– The Jackson Laboratory<br />
<br />
David Hill -– The Jackson Laboratory<br />
<br />
Ira Kalet -– Radiation Oncology, Biomedical Informatics, University of Washington<br />
<br />
Raymond Lee -– Biology, California Institute of Technology<br />
<br />
Jennifer Leopold -– Computer Science, University of Missouri-Rolla <br />
<br />
Suzanna Lewis -– NCBO, Lawrence Berkeley National Laboratory<br />
<br />
Kitsos Louis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas<br />
<br />
Paula Mabee -– Biology, University of South Dakota<br />
<br />
Anne Maglia -– Biological Sciences, University of Missouri-Rolla <br />
<br />
Onard Mejino -– Structural Informatics Group, University of Washington<br />
<br />
Chris Mungall -– NCBO, Lawrence Berkeley National Laboratory<br />
<br />
Fabian Neuhaus -– NCBO, University at Buffalo <br />
<br />
Alan Rector -– Medical Informatics, University of Manchester<br />
<br />
Martin Ringwald -– The Jackson Laboratory<br />
<br />
Cornelius Rosse -– Structural Informatics Group, University of Washington<br />
<br />
Indra Neil Sarkar -– Invertebrate Zoology, American Museum of Natural History<br />
<br />
Nigam Shah -– NCBO, Stanford Medical Informatics<br />
<br />
Barry Smith -– NCBO, University at Buffalo <br />
<br />
David Osumi-Sutherland -– Genetics, University of Cambridge<br />
<br />
Pantelis Topalis -– Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas<br />
<br />
Ravensara Travillian -– Structural Informatics Group, University of Washington<br />
<br />
Peter Vize -– Biology, University of Calgary<br />
<br />
Monte Westerfield -– Institute of Neuroscience, University of Oregon<br />
<br />
== Venue ==<br />
The event will be held in Seattle, WA. Registration and accommodation details will be provided to participants in due course.</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Meetings_and_Events&diff=3764Meetings and Events2006-08-08T00:11:10Z<p>Googlefans: </p>
<hr />
<div>== Upcoming meetings ==<br />
<br />
*'''In Silico Analysis of Proteins. Celebrating the 20th Anniversary of Swiss-Prot'''<br />
**Jul 30- August 4, 2006, Fortaleza, Brazil.<br />
** [http://www.swissprot20.org/ http://www.swissprot20.org/]<br />
** Attending: Michael Ashburner, Suzanna Lewis<br />
<br />
*'''ISMB, 2006'''<br />
**August 6-10, 2006, Fortaleza, Brazil.<br />
** [http://ismb2006.cbi.cnptia.embrapa.br/ http://ismb2006.cbi.cnptia.embrapa.br/]<br />
** Attending: Michael Ashburner, Suzanna Lewis (Keynote speaker for Bio-ontologies SIG)<br />
<br />
*'''IEEE Computational Systems Bioinformatics, 2006'''<br />
*August 14-18, 2006. Stanford University<br />
**[http://www.lifesciencessociety.org/CSB2006/index.html http://www.lifesciencessociety.org/CSB2006/index.html][http://www.wow-gold-sell.com/ wow gold]<br />
** Attending: Mark Musen (Keynote), rest of Stanford group (tutorial in bioontologies/semantic web)<br />
<br />
*'''Tutorial on Standards and Ontologies<br />
**Medical Informatics Europe<br />
**August 27, 2006, Maastricht, Netherlands.<br />
**http://ontology.buffalo.edu/06/MIE_Tutorial.htm<br />
**Attending: Werner Ceusters, Barry Smith<br />
<br />
*'''Anatomy Ontology Workshop'''<br />
**September 8-9, 2006, Seattle<br />
**[[Anatomy Ontology Workshop | information on the Anatomy Ontology Workshop]]<br />
**Attending: Michael Ashburner, Melissa Haendel, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, David Sutherland, Monte Westerfield <br />
<br />
*'''American Society of Human Genetics'''<br />
**October 9-13, 2006, New Orleans, LA<br />
**[http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml http://genetics.faseb.org/genetics/ashg/menu-annmeet.shtml]<br />
**Presentation to find collaborators, also ontology workshop<br />
<br />
*'''Workshop on Philosophy of Biology'''<br />
**October 14-15, 2006, Buffalo, NY<br />
**http://ontology.buffalo.edu/06/pob <br />
**Attending: Werner Ceusters, Barry Smith<br />
<br />
*'''Fall NCBO Project Meeting'''<br />
**Oct. 23-25, 2006, Stanford<br />
** All Hands meeting<br />
** Advisory Comm. & NIH Program & Science officers invited<br />
<br />
*'''Workshop on Ontology of Diseases'''<br />
**In association with FOIS 2006 (Formal Ontology and Information Systems)<br />
**November 6-7, 2006, John Hopkins University, Baltimore<br />
**[[Workshop on Ontology of Diseases | information on the Disease Ontology Workshop]]<br />
**Attending: Werner Ceusters, Christopher Chute, Suzanna Lewis, Chris Mungall, Fabian Neuhaus, Nigam Shah, Barry Smith, Monte Westerfield<br />
<br />
*'''Biomedical Ontology in Action'''<br />
**KR-MED 2006<br />
**November 8, 2006, Baltimore<br />
**http://www.imbi.uni-freiburg.de/medinf/kr-med-2006/index.html<br />
**Attending: Werner Ceusters, Barry Smith<br />
<br />
*'''Tutorial on Genomics Knowledge Representation for Clinical Trials'''<br />
**AMIA Annual Symposium<br />
**November 12, 2006, Washington DC<br />
http://ontology.buffalo.edu/06/AMIAWorkshop.htm <br />
<br />
*'''Panel on the Future of HL7'''<br />
**AMIA Anual Symposium<br />
**November 14, 3.30-5.00pm., Washington DC<br />
**http://ontology.buffalo.edu/HL7/panel.htm<br />
Attending: Barry Smith<br />
<br />
*'''PATO meeting'''<br />
**November 30-December 2, 2006, Stanford University Clark Center<br />
** [[PATO Meeting | information about the PATO Meeting]]<br />
**Attending: Michael Ashburner, Suzanna Lewis, Monte Westerfield<br />
<br />
----<br />
'''2007'''<br />
<br />
*'''Dagstuhl Seminar: Ontology Interoperability in Biomedicine'''<br />
**March 27-30, 2007, Dagstuhl, Germany<br />
**Invitation only<br />
<br />
*'''Workshop on Clinical Trial Ontology'''<br />
**May 16-17 2007, venue TBD<br />
**[[Workshop on Clinical Trial Ontology | information about Clinical Trial Ontology workshop]]<br />
<br />
*'''Training Course on Logical and Computational Tools for Biomedical Ontology Development'''<br />
**June 20-23, 2007: Schloss Dagstuhl, Germany <br />
**Attending: Fabian Neuhaus, Barry Smith.<br />
<br />
*'''Dagstuhl Seminar: Ontologies and Text Mining for Life Sciences'''<br />
**July 23-27, 2007: Schloss Dagstuhl, Germany<br />
**Organizers: Ulf Leser, Dietrich Rebholz-Schuhmann & Michael Ashburner<br />
** Attending: Michael Ashburner<br />
**[http://www.dagstuhl.de/07301 http://www.dagstuhl.de/07301]<br />
<br />
*'''Spatial reasoning over ontologies'''<br />
**Date and Venue tbd<br />
<br />
*'''All NCBCs Ontology workshop'''<br />
**Fall 2007, with Andreas Califano, Columbia, NY<br />
<br />
* '''Phenotype Ontology (Upper Level) workshop'''<br />
**2007?<br />
<br />
== Past meetings ==<br />
<br />
*'''Functional Genomics investigation Ontology (FuGO) 2nd Workshop'''<br />
**July 24-28, 2006, Hinxton, UK<br />
**http://fugo.sourceforge.net/news/index.php<br />
**Attending: Barry Smith<br />
<br />
*'''9th International Protege Conference'''<br />
**July 23-26, 2006, Stanford, CA<br />
**[http://protege.stanford.edu/conference/2006/ http://protege.stanford.edu/conference/2006/]<br />
** Attending: Chris Callendar, Christopher Chute, Tricia d'Entremont, Chris Mungall, Mark Musen, Natasha Noy, Daniel Rubin, Nigam Shah, Kaustubh Supekar<br />
<br />
*'''NCBC All Hands Meeting'''<br />
**July 17-19, 2006, NIH, Bethesda, MD<br />
**Attending: Michael Ashburner, James Buntrock, Chris Callendar, Simona Carini, Louis Goldberg, Deborah McGuinness, Chris Mungall,Mark Musen, Fabian Neuhaus, Daniel Rubin, Nigam Shah, Barry Smith, Nicole Washington, Monte Westerfield <br />
**[http://www.bisti.nih.gov/ahm2006/ http://www.bisti.nih.gov/ahm2006/]<br />
**[http://www.bisti.nih.gov/ahm2006/ncbo_dissemination.htm Ontology: A Vision for the Future and Its Realization] Dissemination Event<br />
***Organizers: Mark Musen, Barry Smith<br />
<br />
* '''Core 1 & 2 Project Meeting'''<br />
** June 27-28, 2006, Berkeley, CA<br />
** Attending: Julie Moseley, Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Christopher Chute, Harold Solbrig (Mayo); Margaret-Anne Storey (UVic); Sherri De Coronado (NIH)<br />
** Working plan for core 1 & 2 goals<br />
<br />
* '''Core 1 & 2 Meeting'''<br />
** June 9, 2006, Berkeley, CA<br />
** Attending: Dilvan Moreira, Lynn Murphy, Daniel Rubin, Nigam Shah, Archana Vembakam (Stanford); Suzanna Lewis, Chris Mungall, ShengQiang Shu, Nicole Washington (Berkeley); James Buntrock, Harold Solbrig (Mayo by phone); Chris Callendar (UVic by phone)<br />
<br />
*'''Training Course in Biomedical Ontologies'''<br />
**[http://ontology.buffalo.edu/06/os2/index.html http://ontology.buffalo.edu/06/os2/index.html]<br />
**May 21-24, 2006, Schloss Dagstuhl, Germany<br />
**Attending: Werner Ceusters, Mark Musen, Barry Smith<br />
<br />
*'''NSF/RCN workshop on ontology and phylogeny'''<br />
**May 21-24, St. Louis, MO<br />
**Attending: Michael Ashburner, Suzanna Lewis, Monte Westerfield<br />
<br />
*'''Phenotype Annotation Meeting'''<br />
**May 17-20, Hinxton, UK<br />
**Attending: Michael Ashburner, Mark Gibson, George Gkoutos, Suzanna Lewis, Gillian Millburn, Chris Mungall, Fabian Neuhaus, Erik Segerdell, Nigam Shah, Monte Westerfield<br />
**[[Agenda PaTO | PATO meeting agenda]]<br />
<br />
*'''Fish Evolutionary Biology Working Group Meeting'''<br />
**April 9-11, National Evolutionary Synthesis Center (NESCent), Durham, NC<br />
**Attending: Mark Gibson,Paula Mabee, Chris Mungall, Monte Westerfield<br />
<br />
*'''Gene Ontology Workshop'''<br />
**March 31-April 3, 2006, St. Croix<br />
** Attending: Michael Ashburner, Suzanna Lewis, Chris Mungall, Barry Smith<br />
<br />
* '''Bio-IT LifeSciences Conference'''<br />
**April 3-6, 2006, Boston, MA'''<br />
**[http://www.lifesciencesexpo.com/live/26/ http://www.lifesciencesexpo.com/live/26/]<br />
** Speaker: Michael Ashburner, Ben Franklin Award Lecture.<br />
<br />
*'''Workshop on Ontology of Images'''<br />
**March 24-25, 2006, Stanford, CA<br />
**[http://www.loni.ucla.edu/CCB/ CCB NCBC] and others with biomedical image ontologies<br />
**[Workshop on Ontology of Images | info on Ontology of Images workshop]<br />
** Attending: Suzanna Lewis, Chris Mungall, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith, Kaushtubh Supekar<br />
<br />
*'''Immunology Ontology Workshop: NIAID'''<br />
**March 21-22, 2006, Gaitherburg, MD<br />
** Attending: Suzanna Lewis (speaker), Mark Musen (Session chair), Barry Smith<br />
<br />
*'''Semantic Technology Conference'''<br />
**March 6-9, 2006, San Jose, CA<br />
** [http://www.semantic-conference.com/ http://www.semantic-conference.com/ ]<br />
** Attending: Deborah McGuinness (Keynote, tutorial), Mark Musen (speaker), Daniel Rubin, Kaustubh Superkar (speaker) <br />
<br />
*'''NIH NCRR Animal Models workshop'''<br />
**March 6-7, 2006, Bethesda, MD<br />
** Attending: Monte Westerfield<br />
<br />
*'''[[Minutes & presentations, March 2-4, 2006 Project meeting|cBio Project Meeting]]'''<br />
**March 2-4, 2006, Stanford, CA<br />
** [[Agenda, Project Meeting, Thursday, March 2-Saturday, March 4, 2006|Agenda]]<br />
**[http://www.smi.stanford.edu/research/cbio/cbio_meeting.html http://www.smi.stanford.edu/research/cbio/cbio_meeting.html]<br />
**Entire project, NIH Program & Lead Science officers <br />
<br />
*'''BIRN ontology workshop'''<br />
**February 28-March 1, 2006, Stanford, CA<br />
** Attending: Christopher Chute, Suzanna Lewis, Mark Musen, Daniel Rubin, Nigam Shah, Barry Smith<br />
<br />
*'''NLM vocabulary collection and distribution meeting'''<br />
**February 27-28, 2006, NLM, Washington, DC<br />
** Attending: James Buntrock, Christopher Chute, Tom Johnson, Chris Mungall, Deepak Sharma, Harold Solbrig<br />
<br />
*'''NIAID meeting'''<br />
**February, 2006, Washington, DC<br />
**Attending: Mark Musen<br />
<br />
*'''cBio Phenotype Annotation tool specification'''<br />
**February 21-23, 2006, Berkeley, CA<br />
** Attending: Melissa Haendel, Sierra Taylor (ZFIN); John Day-Richter, Mark Gibson, Suzanna Lewis, Chris Mungall, ShengQiang Shu (Berkeley)<br />
<br />
*'''Mini-Syposium on Semantic Enrichment of Scientific Literature'''<br />
**February 20, 2006 at the European Bioinformatics Institute, Hinxton, UK<br />
**Attending: Michael Ashburner (speaker)<br />
<br />
*'''cBio OBD specification'''<br />
**February 17, 2006, Berkeley, CA<br />
** Attending: Ben Olasov, Ida Sim (UCSF); Mark Gibson, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); Daniel Rubin (Stanford by phone)<br />
<br />
*'''FuGO meeting'''<br />
** February 13-15, 2006, Philadelphia, PA<br />
**[http://fugo.sourceforge.net/news/index.php http://fugo.sourceforge.net/news/index.php]<br />
**Attending: Barry Smith<br />
<br />
*'''Fourth Semantic Interoperability for E-Government Conference'''<br />
** February 9-10, 2006, MITRE, McLean, VA<br />
** [http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910 http://colab.cim3.net/cgi-bin/wiki.pl?FourthSemanticInteroperabilityforEGovernmentConference_2006_2_0910]<br />
**Attending: Barry Smith<br />
<br />
*'''NIAID BRC3 and Inter Operability Working Group meeting'''<br />
** February 6-7, 2006, Philadelphia, PA<br />
** [http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm http://www.niaid.nih.gov/dmid/genomes/brc/brc3.htm]<br />
** Attending: Suzanna Lewis, Barry Smith<br />
<br />
*'''PharmGKB and cBiO meeting'''<br />
** January 31, 2006, Stanford, CA<br />
** Attending: Daniel Rubin (Stanford); Suzanna Lewis, Sima Misra (Berkeley); Russ Altman, Tina Boussard, Teri Klein, Mark Woon (PharmGKB)<br />
<br />
*'''Pacific Symposium on Biocomputing, 2006'''<br />
**January 2-6, 2006, Maui, HI<br />
**Michael Ashburner (Keynote)<br />
**[http://psb.stanford.edu/ http://psb.stanford.edu/]<br />
<br />
*'''NCBC Meeting'''<br />
**Dec. 15-16, NIH, Bethesda, MD<br />
**Attending: Mark Musen, Suzanna Lewis, Monte Westerfield<br />
**Introducting new NCBCs to each other and NIH staff<br />
<br />
*'''Phenotype Annotation Meeting''' <br />
**December 11-12, 2005, [http://www.visitasilomar.com/ Asilomar conference center]<br />
** Attending: Melissa Haendel, Paula Mabee, Erik Segerdell, Monte Westerfield (ZFIN); Gillian Millburn (FlyBase); Mark Gibson, Suzanna Lewis, Chris Mungall (Berkeley); Chris Callendar, Sean Falconer, Margaret-Anne Storey (UVic)<br />
** Define requirements of phenotype annotation tools<br />
<br />
*'''International Biocurator Meeting'''<br />
**December 8-11, 2005, Asilomar, CA<br />
**[http://biocurator.org/intnlbiocurator.html http://biocurator.org/intnlbiocurator.html]<br />
**Attending: Sima Misra (organizer), Chris Mungall (speaker), Monte Westerfield (speaker)<br />
<br />
*'''National Bioinformatics Network, South Africa'''<br />
**December 2, 2005, University of Cape Town, SA<br />
**Michael Ashburner (Keynote)<br />
<br />
*'''Phenotype Ontology Content Workshop'''<br />
**Nov. 19-20, 2005, Cold Spring Harbor, NY<br />
** Attending: Michael Ashburner, John Day-Richter, George Gkoutos, Suzanna Lewis, Chris Mungall, Mark Musen, Erik Segerdell, Nigam Shah, Monte Westerfield <br />
** [[Media:PhenoAgenda.doc]]<br />
<br />
*'''Stanford/Mayo/Berkeley Meetings'''<br />
**Nov. 21, 10am-3pm, Stanford, CA; Nov. 22, 10am-3pm, Berkeley, CA<br />
** Attending: Lynn Murphy, Mark Musen, Daniel Rubin, Nigam Shah, Archana Vembakam, (Stanford); Nomi Harris, Suzanna Lewis, Sima Misra, Chris Mungall, ShengQiang Shu (Berkeley); James Buntrock, Deepak Sharma, Harold Solbrig (Mayo by phone)<br />
<br />
*'''Forbes Dewey Meeting'''<br />
**Late October, MIT, Cambridge, MA<br />
**Michael Ashburner, chair<br />
**Goal to see if anonymous foundation would pay for ontology content unification, standards, collaboration, etc.<br />
<br />
*'''Genome Informatics Meeting'''<br />
**Oct. 28-Nov. 1, 2005, Cold Spring Harbor, NY<br />
**Suzanna Lewis (organizer, speaker)<br />
<br />
*'''Workshop on Bio-Ontologies'''<br />
**October 28, 2005, Buffalo, NY<br />
**[http://ontology.buffalo.edu/05/bio-ontologies.pdf http://ontology.buffalo.edu/05/bio-ontologies.pdf]<br />
**Presenting: Suzanna Lewis, Frank Hartel, Sumi Yoshikawa, Olivier Bodenreider, David Hill<br />
**Training session: making ontologies better<br />
<br />
*'''1st International Annual Conference, Brazilian Association for Bioinformatics and Computational Biology'''<br />
**October, 2005, Caxambu, Brazil<br />
**Michael Ashburner (Keynote)<br />
<br />
*'''Applied Biosystems Inc., Science Meeting'''<br />
**September, 2005, Asilomar, CA<br />
**Michael Ashburner (Keynote)<br />
<br />
*'''MGED8, Bergen'''<br />
**September, 2005<br />
**Michael Ashburner (Keynote)</div>Googlefanshttps://www.bioontology.org//mediawiki/index.php?title=Workshop_on_Ontology_of_Images&diff=3763Workshop on Ontology of Images2006-08-08T00:11:03Z<p>Googlefans: </p>
<hr />
<div>[[Presentations|Imaging Workshop Slides]]<br />
<br />
[[#Some Relevant Links|Some Relevant Links]] <br />
<br />
== Background ==<br />
<br />
The [http://ncbo.us National Center for Biomedical Ontology] will host a two-day workshop focused on the ontology of (biomedical) images and imaging. The workshop will take place on March 24-25, 2006 in Room M-112 of the [http://lane.stanford.edu/about/directions.html Lane Medical Library] in Stanford. <br />
<br />
The goal of the workshop is to promote interoperability of biomedical image and imaging ontologies through the application of principles of sound ontology construction and through the coordination of current ontology development efforts in the imaging domain. One subsidiary goal is to ensure compatibility of image ontologies with ontologies of those biomedical entities which images represent. The workshop will include hands-on experiments directed towards building a biomedical image ontology on the basis of sample ontologies submitted by participants in advance.<br />
<br />
The following topics will be addressed:<br />
<br />
- coordination and integration of ontologies in the imaging domain<br />
<br />
- ontologies for classification of images, image features, interpretations, <br />
<br />
- the role of a reference ontology such as the [http://sig.biostr.washington.edu/projects/fm/AboutFM.html FMA] <br />
<br />
- the use of common relations (along the lines advanced in the [http://genomebiology.com/2005/6/5/R46 OBO Relation Ontology])[http://www.wow-gold-sell.com/ wow gold], including relations among images, features, interpretations, and the underlying reality<br />
<br />
- use of ontologies in reasoning<br />
<br />
- building an ontology of imaging tools and data, including issues related to the classification of imaging algorithms and to the potential uses of a tools ontology in supporting interoperability of bioinformatics software (in conjunction with the [http://na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group Software and Data Integration Working Group] of the NIH Roadmap National Centers for Biomedical Computing).<br />
<br />
The workshop is designed to be of value to all those involved in biocomputing in the imaging domain, including representatives of those NCBCs who use or develop imaging technologies. <br />
<br />
This workshop was funded by the United States National Institutes of Health (NIH) through the NIH Roadmap for Medical Research, Grant 1 U 54 HG004028. Information on the National Centers for Biomedical Computing can be found at [http://nihroadmap.nih.gov/bioinformatics http://nihroadmap.nih.gov/bioinformatics]. Additional support has been provided by GlaxoSmithKline (GSK), Language & Computing (L&C) and Agfa.<br />
<br />
== Workgroups and Mailing List ==<br />
<br />
At the conclusion of the workshop, many participants expressed interest in continuing the discussions and undertaking the work related to imaging ontology. A mailing list for these discussions was set up (https://www.neuroinformatics.org/mailman/listinfo/image-ontology)<br />
<br />
In addition, a Wiki to host materials related to a working group in imaging ontology was created (http://www.neuroinformatics.org:8080/xwiki/bin/view/ImageOntology/Main). Please visit this Wiki to obtain current information on the projects and activities related to these efforts.<br />
<br />
== Agenda ==<br />
<br />
'''Session I: How to Build an Ontology''' Barry Smith (Moderator) <br />
<br />
9:00am Introduction <br />
<br />
-- What this Meeting is For <br />
<br />
-- Basic Principles of Ontology Design <br />
<br />
-- The OBO Foundry Project <br />
<br />
-- The OBO Relation Ontology <br />
<br />
10:30am Coffee <br />
<br />
11:00am Towards an Ontology for the Imaging Domain <br />
<br />
-- BIRNLex and RadLex Case Studies <br />
<br />
12:15pm Kaustubh Supekar: An Overview of the Groups Represented at this Meeting <br />
<br />
12:30pm Lunch <br />
<br />
'''Session II: Imaging Terms and Relations''' <br />
Daniel Rubin (Moderator) <br />
<br />
1:30pm Participant self-introductions <br />
<br />
2:00pm Ontologies and Terminologies in Radiology and Biological Imaging <br />
<br />
-- Curt Langlotz: RadLex <br />
<br />
-- Maryann Martone: BIRNLex <br />
<br />
-- Anand Kumar: DICOM <br />
<br />
3:30pm Coffee <br />
<br />
4:00pm Relations and Reasoning in Image Ontologies <br />
<br />
-- Dirk Marwede: Relations in Image Ontologies and Anatomy Ontologies <br />
<br />
-- Mariana Casella dos Santos: Bootstrapping an Image Ontology <br />
<br />
-- Helen Chen: Building Real-World Applications and Reasoning in Radiology <br />
<br />
'''Session III: Image Ontologies''' <br />
Suzanna Lewis (Moderatrix) <br />
<br />
9:00am Examples <br />
<br />
-- Matthew Fielding: From RadLex to RadiO <br />
<br />
-- C. Forbes Dewey: Experibase <br />
<br />
10:30am Coffee <br />
<br />
11:00am Reasoning with Image Ontologies <br />
<br />
-- W. Lorensen: Engineering Beyond Pixels <br />
<br />
-- William Bug: BIRN's Image Ontology Requirements <br />
<br />
-- Louis Goldberg: On Reasoning with Images <br />
<br />
12:30pm Lunch <br />
<br />
'''Session IV: Imaging Tools and Data''' <br />
Ivo Dinov and Barry Smith (Moderators) <br />
<br />
1:30pm Towards an Ontology of Imaging Tools and Data <br />
<br />
-- David Kennedy: The Internet Analysis Tools Registry <br />
<br />
-- Barry Smith: What Should an Ontology of Tools and Data Look Like? <br />
<br />
-- Ontology vs. Yellow Pages: Concluding Debate between Ivo Dinov, Peter Lyster, Suzanna Lewis and Bill Lorensen<br />
<br />
3:30pm Coffee <br />
<br />
-- Strategy Session: How to Build an Image Ontology<br />
<br />
== Participants ==<br />
<br />
Yasser alSafadi (Philips Research)<br />
<br />
Carol Bean (NCRR)<br />
<br />
Bruce Bray (Utah) <br />
<br />
William Bug (BIRN)<br />
<br />
James A Butler (GlaxoSmithKline)<br />
<br />
David Channin (NMH)<br />
<br />
Helen Chen (Agfa)<br />
<br />
Beverly Collins (Radlex) <br />
<br />
Sherri de Coronado (NCI)<br />
<br />
C. Forbes Dewey (MIT)<br />
<br />
Ivo Dinov (UCLA)<br />
<br />
Keith Dreyer (Harvard)<br />
<br />
Matthew Fielding (IFOMIS)<br />
<br />
Daniel Gardner (Cornell)<br />
<br />
Christine Golbreich (Rennes)<br />
<br />
Louis Goldberg (Buffalo)<br />
<br />
Jeff Grethe (BIRN)<br />
<br />
Ammar Halawa (FujiFilm Medical Systems)<br />
<br />
Donald Harrington (NIBIB)<br />
<br />
David Hellman (L&C) <br />
<br />
Peter Hunter (Aukland)<br />
<br />
David Kennedy (Harvard)<br />
<br />
Richard I. Kitney (Imperial College, London)<br />
<br />
Anand Kumar (IFOMIS)<br />
<br />
Curtis Langlotz (University of Pennsylvania)<br />
<br />
Suzanna Lewis (Berkeley)<br />
<br />
William Lorensen (General Electric)<br />
<br />
Peter F. Lyster (NIH/NIGMS)<br />
<br />
Maryann Martone (BIRN)<br />
<br />
Dirk Marwede (IFOMIS / Department of Radiology, University of Leipzig)<br />
<br />
Jose L. Mejino, Jr. (Foundational Model of Anatomy)<br />
<br />
John Michon (Duke)<br />
<br />
Chris Mungall (Berkeley)<br />
<br />
Robert Murphy (CMU)<br />
<br />
Mark Musen (Stanford)<br />
<br />
Dianne Reeves (NCI)<br />
<br />
Jens Rittscher (GE)<br />
<br />
Daniel Rubin (Stanford)<br />
<br />
Mariana Casella Dos Santos (L&C, Belgium)<br />
<br />
Nigam Shah (Stanford)<br />
<br />
Ken Shastri (FujiMed)<br />
<br />
Barry Smith (Buffalo)<br />
<br />
Kaushtubh Supekar (Stanford)<br />
<br />
== Webcast ==<br />
<br />
Session I<br />
Barry Smith (Moderator)<br />
<br />
'''How to Build an Ontology''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-09.ram<br />
<br />
'''Towards an Ontology for the Imaging Domain'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-11.ram<br />
<br />
<br />
Session II <br />
Daniel Rubin (Moderator)<br />
<br />
'''Imaging Terms and Relations''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1330.ram<br />
<br />
'''Relations and Reasoning in Image Ontologies'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-24-2006-1600.ram<br />
<br />
<br />
Session III <br />
Suzanna Lewis (Moderatrix)<br />
<br />
'''Image Ontologies''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-09.ram<br />
<br />
'''Reasoning with Image Ontologies'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-11.ram<br />
<br />
<br />
Session IV <br />
Ivo Dinov and Barry Smith (Moderatores)<br />
<br />
'''Imaging Tools and Data''' <br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1330.ram<br />
<br />
'''Ontology vs. Yellow Pages'''<br />
<br />
http://med.stanford.edu/irt/mmt/video/ontology/ontology-03-25-2006-1600.ram<br />
<br />
== Some Relevant Links ==<br />
<br />
[http://genomebiology.com/2005/6/5/R47 The Open Microscopy Environment (OME) Data Model]<br />
<br />
[http://obo.sourceforge.net/cgi-bin/detail.cgi?image OBO Biological Imaging Methods]<br />
<br />
[http://www.rsna.org/Radlex/index.cfm RadLex: A Lexicon for Uniform Indexing and Retrieval of Radiology Information Resources]<br />
<br />
[http://medical.nema.org/ DICOM]<br />
<br />
[http://nifti.nimh.nih.gov/ Neuroimaging Informatics Technology Initiative]<br />
<br />
[http://www.dclunie.com/ David Clunie's Medical Image Format Site]<br />
<br />
[http://www.library.uthscsa.edu/internet/ImageDatabases.cfm Medical Image Databases]<br />
<br />
[http://www.pathbase.net/Pathbase/ Mutant Mouse Images]<br />
<br />
[http://sig.biostr.washington.edu/projects/fm/AboutFM.html Foundational Model of Anatomy]<br />
<br />
[http://www.structuredreporting.com/ Structured Reporting]<br />
<br />
[http://murphylab.web.cmu.edu/services/ Murphy Lab Image Services]<br />
<br />
[https://cabig.nci.nih.gov/workspaces/Imaging In Vivo Imaging]<br />
<br />
[http://www.cl.cam.ac.uk/%7Eafb21/publications/TwD98.html A Taxonomy of Diagram Taxonomies]<br />
<br />
[http://www.bioimage.org/ Bioimage Database]<br />
<br />
[http://www.brainmap.org/ BrainMap:A Functional Neuroimaging Database]<br />
<br />
<br />
== Tool Registries ==<br />
<br />
[http://www.cma.mgh.harvard.edu/iatr/ Registry of Image Analysis Tools]<br />
<br />
[http://www.brc-central.org/tdb/prok_manatee/brc-central/software.shtml BRC Central Bioinformatics Resource Center]<br />
<br />
<br />
----<br />
<br />
[[Hotel]]<br />
<br />
[[Venue]]</div>Googlefans