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From: Nigam S. <ni...@st...> - 2013-04-04 20:11:24
|
_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Chiara D. V. <wom...@ea...> - 2013-03-15 17:18:18
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========================================================
7th Int'l Workshop on Modular Ontologies (WoMO)
Corunna, Spain, September, 2013
held in conjunction with LPNMR 2013
--- First Call for Papers ---
========================================================
Submission deadline: July 5, 2013
========================================================
http://www.iaoa.org/womo/2013.html
MODULARITY, studied for years in software engineering, allows mechanisms
for easy and flexible reuse, generalization, structuring, maintenance,
design patterns, and comprehension. In formal and applied ontology,
modularity is central to reducing the complexity of designing and
understanding ontologies, and to facilitating ontology verification,
reasoning, development, maintenance and integration.
Recent research on ontology modularity shows substantial progress in
foundations of modularity, techniques of modularization and modular
development, distributed reasoning and empirical evaluation. These results
provide a solid foundation and exciting prospects for further research and
development.
The workshop continues a series of successful events that have been an
excellent venue for practitioners and researchers to discuss latest and
current work. The most recent WoMOs were held at ESSLLI 2011 and FOIS/ICBO
2012. This time WoMO is organised as a workshop of LPNMR 2013: the 12th
International Conference on Logic Programming and Non-monotonic Reasoning.
LPNMR is well-established as the main conference in the field.
The workshop will be open to all attendants of LPMNR'13 and its workshops.
Workshop speakers will be required to register for WoMO via the LPMNR'13
website. Registration for WoMO only will be possible.
TOPICS include, but are not limited to:
- What is modularity?: kinds of modules and their properties; modules vs.
contexts; design patterns; granularity of representation;
- Logical/foundational studies: modular ontology languages; reconciling
inconsistencies across modules; formal structuring of modules;
heterogeneity; hybrid theories; intertheory relations (conservativity,
interpretability, strong equivalence, inseparability, etc.)
- Algorithmic approaches: distributed and incremental reasoning;
modularization and module extraction; sharing, linking, reuse; privacy;
complexity of reasoning; implemented systems;
- Evaluation of modularizations: case studies or other analyses of ontology
modularizations (why it is modularized in a certain way, what does it
address, how can it be improved); how to measure the adequacy of a
modularization; comparison of modularizations with respect to
philosophical, logical, reasoning, cognitive, or social aspects;
- Applications: semantic web; life sciences; earth sciences;
bio-ontologies; natural language processing; space and time; ambient
intelligence; social intelligence; technology and engineering;
collaborative ontology development and ontology versioning.
IMPORTANT DATES
Paper Submission: July 5, 2013
Notification: August 19, 2013
Camera ready: September 2, 2013
Workshop: September 15, 2013
SUBMISSION GUIDELINES:
We welcome submissions on modularity in a broad sense. The workshop is open
to papers of theoretical or practical nature from various disciplines.
Submissions can be long papers (11 pages) or short papers (5 pages),
formatted according to Springer LNCS style (see
http://www.springer.com/comp/lncs/Authors.html), prepared in PDF format and
submitted no later than the submission deadline, through the EasyChair
Submission System (see http://www.easychair.org/conferences/?conf=womo2013).
Submitted papers will be peer-reviewed by members of the program committee.
Accepted papers will be made available in the proceedings to be published
electronically in the CEUR Workshop Proceedings series (see
http://www.ceur-ws.org). Find proceedings of WoMO 2011 and 2012 at
http://www.booksonline.iospress.nl/Content/View.aspx?piid=20369 and at
http://ceur-ws.org/Vol-875/)
WORKSHOP CHAIRS:
Torsten Hahmann, University of Toronto, Canada
David Pearce, Universidad Politecnica de Madrid, Spain
Chiara Del Vescovo, University of Manchester, UK
Dirk Walther, TU Dresden, Germany
PROGRAM COMMITTEE: TBA
INVITED SPEAKERS: TBA
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From: Nigam S. <ni...@st...> - 2013-03-13 20:43:14
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Nigam S. <ni...@st...> - 2013-02-22 03:03:21
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Pierre L. <pie...@ir...> - 2013-02-08 18:09:53
|
(Apologies for multiple reception of this message)
CALL FOR PAPERS
---------------------------------------------------------
1st International Workshop on
Semantics for Biodiversity (S4BIODIV)
http://semantic-biodiversity.mpl.ird.fr/
---------------------------------------------------------
Held in parallel with
the 10th Extended Semantic Web Conference (ESWC 2013)
http://2013.eswc-conferences.org/
Montpellier, France, May 26/27, 2013
WORKSHOP DESCRIPTION
---------------------------------------------------------
The semantic Web standards, tools, ontologies and related technologies have considerably grown in maturity in the recent years. Nowadays, accessing a wide catalog of biological, social, environmental, ecological data sources allows supporting the Biodiversity stakeholders to resolve their complex questions. Will the real time access to web resources efficiently support the definition of strategies to conserve and manage biodiversity? How semantic web technologies could help handling the complex and heterogeneous big data related to Biodiversity?
The workshop aims at indentifying the key challenges faced by the bioinformatics community, discuss the solutions and identify the opportunities emerging from the trans-disciplinary interactions (Plant Science – Informatics). Therefore, we expect the bioinformatics experts to explain how they apply semantic web standards and tools to their scientific topic, from Biology, Agro-ecology, Genomics, Environment, to Social Sciences, Citizen Sciences.
Research papers presenting various aspects of Semantic Web technologies applied to Biodiversity data, ranging from position papers to implemented systems description and their evaluation, will be selected. We are particularly interested by the use of the semantic technologies to design, develop systems that supports research on Biodiversity conservation and management for food security, (like the strategies for resilience to climate change pressure, sustainability of productive ecosystems, ecosystems services monitoring, territories management, etc.), rather than systems only supporting research on climate patterns, soil erosion, and the potential consequences on biodiversity.
TOPICS
------
------
Scientific themes of interest (include but are not limited to):
* sustainable agriculture,
* plant,
* health and habitat,
* relationship between plant-pests/pathogens,
* usages of plants by community,
* biodiversity conservation,
* ecosystems services,
* quality of biodiversity data.
Informatics technologies of interest (include but are not limited to):
* ontology applications,
* knowledge engineering,
* linked biodiversity data,
* remote sensors,
* mobile devices,
* vizualization tools,
* data mining.
ABSTRACT & PAPER SUBMISSION DETAILS:
------------------------------------
------------------------------------
Authors are invited to submit electronically original contributions in English. Authors must send a pre-submission abstract not exceeding 500 words at s4b...@ir.... Authors will receive a mail indicating of their abstract has been selected by the Scientific Committee for a full paper submission.
Submitted papers should not exceed 15 pages for long papers and 8 pages for short papers and must be formatted according to the LNCS guidelines.
Submissions will only be accepted in the PDF format. Submissions must be realized through the easychair system at
http://www.easychair.org/conferences/?conf=s4biodiv2013
IMPORTANT DATES:
----------------
----------------
Pre-submission inquiry deadline: February 24, 2013
Submission Deadline: March 4, 2013.
Notification: April 1, 2013
Camera ready: April 15, 2013.
Workshop day: May 26/27, 2013.
PUBLICATION:
------------
------------
Proceedings of the workshop will be published online at CEUR Workshop Proceedings (CEUR-WS.org). The best paper presented at the workshop will be included in the supplementary Springer LNCS proceedings of the ESWC2013 conference. Furthermore, a selection of papers presented at the workshop will be invited to be revised and extended version for a second peer-review process targeting publication in a referenced journal.
INFORMATION:
------------
------------
The workshop will take place in Montpellier, May 26/27, 2013.
Please visit the website for more information:
http://semantic-biodiversity.mpl.ird.fr/
STEERING COMMITEE:
Pierre Larmande (IRD - UMR DIADE, France) (Chair)
Isabelle Mougenot (UMII – UMR Espace DEV, France)
Thérèse Libourel (UMII – UMR Espace DEV, France)
Clément Jonquet (UMII – LIRMM, France)
SCIENTIFIC COMMITTEE:
Elizabeth Arnaud (Bioversity International, France) (Chair)
Manuel Ruiz (CIRAD - UMR AGAP, France)
Pierre Bonnet (CIRAD - UMR AMAP, France)
Richard Bruskiewich (Bioversity International, Italy)
Pascal Neveu (INRA - UMR MISTEA, France)
Joel Sachs (University of Maryland, Baltimore County, USA)
Julie Chabalier (Natural Solutions, France)
Cyril Pommier (INRA - URgi – Ephesis, France)
Mark Wilkinson (Polytechnic University of Madrid, and University of British Columbia)
Konstantin Todorov (UMII - UMR LIRMM, France)
Pankaj Jaiswal (Oregon State University, USA)
Xavier Sirault (CSIRO, Autralia)
Caterina Caracciolo (FAO , Italy)
Lieke Verhelst (Wageningen University, The Netherlands)
Damian Gessler (Iplant collaborative, USA)
Nikos Manouselis (Agro-Know, University of Alcala, Grece)
Éamonn Ó Tuama (GBIF, University of Copenhagen , Denmark)
-----
Pierre Larmande
Workshop Semantics for Biodiversity
Steering Committee and Organization Committee Chair
http://semantic-biodiversity.mpl.ird.fr/
PhD in computational biology
Member of the Institute of Computational Biology
http://www.ibc-montpellier.fr/
Correspondant du plateau bioinformatique
http://bioinfo.mpl.ird.fr/
IRD - UMR DIADE
911 avenue Agropolis,
BP 64501
34394 Montpellier cedex 5
pie...@ir...
04 67 41 62 90
_______________________________________________
bioportal-announce mailing list
bio...@li...
https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
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From: Paea L. <ple...@st...> - 2013-02-07 18:50:51
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Nigam S. <ni...@st...> - 2013-02-07 00:52:36
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Ray F. <ray...@st...> - 2013-02-06 18:49:30
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Trish W. <wh...@st...> - 2013-02-01 01:31:18
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Trish W. <wh...@st...> - 2013-01-30 19:15:43
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Ray F. <ray...@st...> - 2012-11-01 23:17:06
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_______________________________________________ bioportal-announce mailing list bio...@li... https://mailman.stanford.edu/mailman/listinfo/bioportal-announce |
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From: Cynthia S. <Cyn...@ja...> - 2012-10-26 20:20:14
|
My apologies for the “reply all” vs “reply” error. It’s late Friday afternoon. Cynthia The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. |
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From: Cynthia S. <Cyn...@ja...> - 2012-10-26 20:17:30
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Hi Melissa- For the Mammalian Phenotype Ontology, I will be the contact. I am already subscribed to the OBO-Discuss list, but I should perhaps look at it more regularly from here on out. We would also like to update our listserve address from ph...@in... to ph...@ja.... While the old address still works for now, we do not know when/if this will be deactivated. We are also considering how best to comply with setting a data version tag, -many decisions to be made here so I do not have a time frame for implementation just yet. Best, Cynthia Cynthia Smith, Ph.D. Senior Scientific Curator The Jackson Laboratory Mouse Genome Informatics Bx-45 600 Main Street Bar Harbor, ME 04609 USA www.informatics.jax.org email: Cyn...@ja... Phone: (207) 288-6663 Fax: (207) 288-6131 Skype: clsjey On 10/26/12 2:04 PM, "Melissa Haendel" <ha...@oh...> wrote: Hi all, The OBO Foundry is currently working on some new and improved ontology management strategies. As these strategies and infrastructure mature, we will be making announcements on the OBO-Discuss mailing list and contacting each ontology steward. Because this listserve is currently listed as a contact for an OBO Foundry registered ontology, we would request that someone on this list please suggest a contact person. Please note that we will continue to maintain links to these associated listserves. Each ontology contact/steward (regardless if OBO or OWL) should subscribe to obo-discuss. You can do so here: https://lists.sourceforge.net/lists/listinfo/obo-discuss We would be grateful for your help in accomplishing our goal of having a contact person for each OBO ontology registered with the Foundry. On behalf of the OBO Foundry, Melissa Dr. Melissa Haendel Assistant Professor Ontology Development Group, OHSU Library http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology Oregon Health & Science University ha...@oh... skype: melissa.haendel 503-407-5970 The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. |
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From: Melissa H. <ha...@oh...> - 2012-10-26 18:05:09
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Hi all, The OBO Foundry is currently working on some new and improved ontology management strategies. As these strategies and infrastructure mature, we will be making announcements on the OBO-Discuss mailing list and contacting each ontology steward. Because this listserve is currently listed as a contact for an OBO Foundry registered ontology, we would request that someone on this list please suggest a contact person. Please note that we will continue to maintain links to these associated listserves. Each ontology contact/steward (regardless if OBO or OWL) should subscribe to obo-discuss. You can do so here: https://lists.sourceforge.net/lists/listinfo/obo-discuss We would be grateful for your help in accomplishing our goal of having a contact person for each OBO ontology registered with the Foundry. On behalf of the OBO Foundry, Melissa Dr. Melissa Haendel Assistant Professor Ontology Development Group, OHSU Library http://www.ohsu.edu/library/ Department of Medical Informatics and Epidemiology Oregon Health & Science University ha...@oh...<mailto:ha...@oh...> skype: melissa.haendel 503-407-5970 |
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From: Chris M. <cjm...@lb...> - 2012-08-30 16:37:29
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imports are unfortunately not well supported by obo-edit. OWL is best for working with multiple ontologies. Oort can be used to generate versions of ontologies that have subsets of other ontologies merged in. UO should be released this way - can you do this George? On Aug 30, 2012, at 8:24 AM, Matthew Chambers wrote: > Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and > pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the > terms that belong to that ontology, translated to lowercase." > > But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same > semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to > figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers > are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... > > -Matt > > > On 8/30/2012 10:02 AM, George Gkoutos wrote: >> >> Hi Gerhard, >> >> the error you are getting is due to the lack of the pato import. Without >> being 100% sure, I suspect it has nothing to do with the new OBO format. >> >> Couple of things you could do to solve this: >> >> 1. Import PATO as a separate ontology - this should solved the error you >> are getting, >> 2. If you do not want to import PATO - when you try to load the ontology >> click on the advance option and select the "Avoid dangling references" >> option. This would stop oboedit complaining about the missing PATO terms. >> >> Please let me know if this works for you. >> >> Best wishes, >> >> George >> >> On 30/08/2012 11:45, Gerhard Mayer wrote: >>> Hallo Mr. Gkoutos, >>> >>> I'm maintaining the psi-ms.ontology >>> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >>> >>> Since the last release (29:08:2012) of the unit.obo file I get the >>> following errors when I try to load my ontology by OBO-Edit 2.2: >>> >>> Load Error, line 547 48 unrecognized parent terms: >>> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >>> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >>> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >>> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >>> >>> >>> I saw that in former versions of the unit ontology there was the import statement >>> import: http://purl.obolibrary.org/obo/pato.obo >>> which is now missing resp. replaced by >>> ontology: uo >>> ontology: pato >>> >>> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >>> ontology: xyz >>> was introduced as a new docuemnt header tag. >>> >>> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >>> >>> In addition you specified the old 1.2 format in your unit.obo file: >>> format-version: 1.2 >>> which should be changed to >>> format-version: 1.4 >>> in case you want to use the new format. >>> >>> Best Regards, >>> Gerhard >>> >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Obo-unit mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-unit >> > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit |
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From: Chris M. <cjm...@lb...> - 2012-08-30 16:35:56
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On Aug 30, 2012, at 3:45 AM, Gerhard Mayer wrote: > But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. > > In addition you specified the old 1.2 format in your unit.obo file: > format-version: 1.2 > which should be changed to > format-version: 1.4 > in case you want to use the new format. > > Best Regards, > Gerhard Hi Gerhard The story is more complex than that. Every oboformat 1.2 ontology should be a valid 1.4 ontology. There is no formal spec for 1.2, only a rough guide. There is a formal spec for 1.4, and although some aspects of the mapping to owl have the potential to change, the 1.4 formal spec should be regarded as the canonical way to interpret any obo format file. See http://oboformat.org Are you on the obo-format list? I think it's important to have a representative of PSI-MOD there. |
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From: George G. <g.g...@ge...> - 2012-08-30 15:39:55
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On 30/08/2012 16:24, Matthew Chambers wrote: Hi Matt, your are quite right - I have now removed the ontology: pato statement. Best wishes, George > Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and > pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the > terms that belong to that ontology, translated to lowercase." > > But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same > semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to > figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers > are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... > > -Matt > > > On 8/30/2012 10:02 AM, George Gkoutos wrote: >> Hi Gerhard, >> >> the error you are getting is due to the lack of the pato import. Without >> being 100% sure, I suspect it has nothing to do with the new OBO format. >> >> Couple of things you could do to solve this: >> >> 1. Import PATO as a separate ontology - this should solved the error you >> are getting, >> 2. If you do not want to import PATO - when you try to load the ontology >> click on the advance option and select the "Avoid dangling references" >> option. This would stop oboedit complaining about the missing PATO terms. >> >> Please let me know if this works for you. >> >> Best wishes, >> >> George >> >> On 30/08/2012 11:45, Gerhard Mayer wrote: >>> Hallo Mr. Gkoutos, >>> >>> I'm maintaining the psi-ms.ontology >>> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >>> >>> Since the last release (29:08:2012) of the unit.obo file I get the >>> following errors when I try to load my ontology by OBO-Edit 2.2: >>> >>> Load Error, line 547 48 unrecognized parent terms: >>> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >>> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >>> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >>> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >>> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >>> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >>> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >>> >>> >>> I saw that in former versions of the unit ontology there was the import statement >>> import: http://purl.obolibrary.org/obo/pato.obo >>> which is now missing resp. replaced by >>> ontology: uo >>> ontology: pato >>> >>> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >>> ontology: xyz >>> was introduced as a new docuemnt header tag. >>> >>> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >>> >>> In addition you specified the old 1.2 format in your unit.obo file: >>> format-version: 1.2 >>> which should be changed to >>> format-version: 1.4 >>> in case you want to use the new format. >>> >>> Best Regards, >>> Gerhard >>> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Obo-unit mailing list >> Obo...@li... >> https://lists.sourceforge.net/lists/listinfo/obo-unit >> > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit |
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From: Matthew C. <mat...@gm...> - 2012-08-30 15:24:40
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Reading the description of the "ontology" tag, it seems like unit.obo is claiming both the uo and pato namespaces: "The ID space of this ontology. This should correspond to to the ID prefix of the terms that belong to that ontology, translated to lowercase." But then, reading the description of the "import" tag, in 1.4 it is supposed to have the same semantics as the ontology tag. So there's no real import anymore, it's just up to the parser to figure out how to resolve the ids. I think pato should be the URL to the PATO obo though. Parsers are probably more likely to resolve it that way! It sounds like OBO-Edit needs an upgrade though... -Matt On 8/30/2012 10:02 AM, George Gkoutos wrote: > > Hi Gerhard, > > the error you are getting is due to the lack of the pato import. Without > being 100% sure, I suspect it has nothing to do with the new OBO format. > > Couple of things you could do to solve this: > > 1. Import PATO as a separate ontology - this should solved the error you > are getting, > 2. If you do not want to import PATO - when you try to load the ontology > click on the advance option and select the "Avoid dangling references" > option. This would stop oboedit complaining about the missing PATO terms. > > Please let me know if this works for you. > > Best wishes, > > George > > On 30/08/2012 11:45, Gerhard Mayer wrote: >> Hallo Mr. Gkoutos, >> >> I'm maintaining the psi-ms.ontology >> (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). >> >> Since the last release (29:08:2012) of the unit.obo file I get the >> following errors when I try to load my ontology by OBO-Edit 2.2: >> >> Load Error, line 547 48 unrecognized parent terms: >> line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo >> org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) >> org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) >> org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) >> org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) >> org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) >> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) >> org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) >> >> >> I saw that in former versions of the unit ontology there was the import statement >> import: http://purl.obolibrary.org/obo/pato.obo >> which is now missing resp. replaced by >> ontology: uo >> ontology: pato >> >> I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) >> ontology: xyz >> was introduced as a new docuemnt header tag. >> >> But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. >> >> In addition you specified the old 1.2 format in your unit.obo file: >> format-version: 1.2 >> which should be changed to >> format-version: 1.4 >> in case you want to use the new format. >> >> Best Regards, >> Gerhard >> > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit > |
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From: George G. <g.g...@ge...> - 2012-08-30 15:02:53
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Hi Gerhard, the error you are getting is due to the lack of the pato import. Without being 100% sure, I suspect it has nothing to do with the new OBO format. Couple of things you could do to solve this: 1. Import PATO as a separate ontology - this should solved the error you are getting, 2. If you do not want to import PATO - when you try to load the ontology click on the advance option and select the "Avoid dangling references" option. This would stop oboedit complaining about the missing PATO terms. Please let me know if this works for you. Best wishes, George On 30/08/2012 11:45, Gerhard Mayer wrote: > Hallo Mr. Gkoutos, > > I'm maintaining the psi-ms.ontology > (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). > > Since the last release (29:08:2012) of the unit.obo file I get the > following errors when I try to load my ontology by OBO-Edit 2.2: > > Load Error, line 547 48 unrecognized parent terms: > line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo > org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) > org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) > org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) > org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) > org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) > org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) > org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) > > > I saw that in former versions of the unit ontology there was the import statement > import: http://purl.obolibrary.org/obo/pato.obo > which is now missing resp. replaced by > ontology: uo > ontology: pato > > I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) > ontology: xyz > was introduced as a new docuemnt header tag. > > But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. > > In addition you specified the old 1.2 format in your unit.obo file: > format-version: 1.2 > which should be changed to > format-version: 1.4 > in case you want to use the new format. > > Best Regards, > Gerhard > |
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From: Gerhard M. <may...@ru...> - 2012-08-30 10:46:20
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Hallo Mr. Gkoutos, I'm maintaining the psi-ms.ontology (http://psidev.cvs.sourceforge.net/viewvc/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo). Since the last release (29:08:2012) of the unit.obo file I get the following errors when I try to load my ontology by OBO-Edit 2.2: Load Error, line 547 48 unrecognized parent terms: line 83: PATO:0000146 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 568: PATO:0001718 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2665: PATO:0001747 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 49: PATO:0000128 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2079: PATO:0001674 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2783: PATO:0001574 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1880: PATO:0001019 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2655: PATO:0001521 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1114: PATO:0000044 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1332: PATO:0001740 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2684: PATO:0001757 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2623: PATO:0000992 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 2314: PATO:0001682 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 61: PATO:0000165 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1255: PATO:0001414 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1633: PATO:0001717 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1655: PATO:0001299 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 507: PATO:0001709 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 1362: PATO:0001744 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo line 547: PATO:0000033 ofhttp://unit-ontology.googlecode.com/svn/trunk/unit.obo org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1614) org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74) org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:270) org.bbop.dataadapter.DataAdapterOperationTask.execute(DataAdapterOperationTask.java:43) org.bbop.util.AbstractTaskDelegate.run(AbstractTaskDelegate.java:60) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.executeTask(BackgroundEventQueue.java:137) org.bbop.swing.BackgroundEventQueue$BackgroundEventThread.run(BackgroundEventQueue.java:79) I saw that in former versions of the unit ontology there was the import statement import: http://purl.obolibrary.org/obo/pato.obo which is now missing resp. replaced by ontology: uo ontology: pato I saw that in the The OBO Flat File Format Guide, version 1.4 (http://www.geneontology.org/GO.format.obo-1_4.shtml) ontology: xyz was introduced as a new docuemnt header tag. But the OBO Format version 1.4 is to my knowledge until now in DRAFT status. In addition you specified the old 1.2 format in your unit.obo file: format-version: 1.2 which should be changed to format-version: 1.4 in case you want to use the new format. Best Regards, Gerhard -- ------------ Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer Kairos GmbH Universitätsstraße 136 44799 Bochum Email: ger...@ka... |
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From: George G. <g.g...@ge...> - 2012-07-23 14:01:54
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Hi Gerhard, thanks a lot for this - it is now fixed. Best wishes, George On 17 Jul 2012, at 14:03, Gerhard Mayer wrote: > Hello Mr. George Gkoutos, > > I noticed a discrepancy between the two obo-files unit.obo and pato.obo: > > In unit.obo pato-obo is imported via the import statement > http://purl.obolibrary.org/obo/pato.obo > Later in unit.obo the 'unit_of' relationship are used. > > But in pato.obo there is only a relationship 'is_unit_of' defined. > > Is that intended or an error? > If you load unit.obo with OBO-Edit one gets an error by the > VerificationManager because of that. > > Best regards, > Gerhard Mayer > > -- > ------------ > Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer > Kairos GmbH > Universitätsstraße 136 44799 Bochum > Email: ger...@ka... > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Obo-unit mailing list > Obo...@li... > https://lists.sourceforge.net/lists/listinfo/obo-unit |
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From: Gerhard M. <may...@ru...> - 2012-07-17 13:03:50
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Hello Mr. George Gkoutos,
I noticed a discrepancy between the two obo-files unit.obo and pato.obo:
In unit.obo pato-obo is imported via the import statement
http://purl.obolibrary.org/obo/pato.obo
Later in unit.obo the 'unit_of' relationship are used.
But in pato.obo there is only a relationship 'is_unit_of' defined.
Is that intended or an error?
If you load unit.obo with OBO-Edit one gets an error by the
VerificationManager because of that.
Best regards,
Gerhard Mayer
--
------------
Dipl. Inform. med., Dipl. Wirtsch. Inf. Gerhard Mayer
Kairos GmbH
Universitätsstraße 136 44799 Bochum
Email: ger...@ka...
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From: Trish W. <wh...@st...> - 2012-07-14 19:10:50
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From: Trish W. <wh...@st...> - 2012-06-20 00:43:38
|
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From: Trish W. <wh...@st...> - 2012-05-21 22:43:58
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