From sathiyamoorthybioinfo at gmail.com Wed Nov 11 01:20:28 2009 From: sathiyamoorthybioinfo at gmail.com (sathiyamoorthy s) Date: Wed, 11 Nov 2009 15:20:28 +0900 Subject: [Po-dev] Relationship between Gene ontology and Plant ontology-Reg Message-ID: <5492bc760911102220x5e6e13eeg6f3552458d5cc575@mail.gmail.com> Dear plant ontology group, I am sathiyamoorthy s doctoral student from kyung hee university from South Korea, I am interested to give the cross reference of Plant ontology for my transcriptome plant sequences. Is there any relationship between Gene ontology and Plant ontology. can i access the PO using the GO ids.Please help me out. Thank you -- Regards, S.Sathiyamoorthy . -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaiswalp at science.oregonstate.edu Wed Nov 11 15:23:43 2009 From: jaiswalp at science.oregonstate.edu (Pankaj Jaiswal (OSU)) Date: Wed, 11 Nov 2009 12:23:43 -0800 Subject: [Po-dev] Relationship between Gene ontology and Plant ontology-Reg In-Reply-To: <5492bc760911102220x5e6e13eeg6f3552458d5cc575@mail.gmail.com> References: <5492bc760911102220x5e6e13eeg6f3552458d5cc575@mail.gmail.com> Message-ID: <4AFB1D4F.3020200@science.oregonstate.edu> Dear S. Sathiyamoorthy, As of now there is no connection between the GO and PO based on the terms that you may be looking for. Such as find all the molecular functions and processes that are found in leaf, xylem, phloem, SAM, etc. However based on the annotations one can build connections. For this you will have to compare two files e.g. from TAIR for Arabidopsis. We provide the links to GO site database for the respective gene IDs if they exist. #1 Arabidopsis gene annotations for PO http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_temporal_gene_arabidopsis_tair.assoc?revision=724&view=markup and #2 Arabidopsis gene annotations for GO http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/gene_association.tair.gz?rev=HEAD All you may need is to find the AT gene IDs and compare the GO annotation and its localization in a associated PO term. I hope it helps. Pankaj sathiyamoorthy s wrote: > Dear plant ontology group, > > I am sathiyamoorthy s doctoral student from kyung hee university from > South Korea, I am interested to give the cross reference of Plant > ontology for my transcriptome plant sequences. Is there any > relationship between Gene ontology and Plant ontology. can i access the > PO using the GO ids.Please help me out. > > Thank you > > > -- > Regards, > > S.Sathiyamoorthy . > > > ------------------------------------------------------------------------ > > _______________________________________________ > Po-dev mailing list > Po-dev at plantontology.org > http://mail.plantontology.org/mailman/listinfo/po-dev -- Pankaj Jaiswal Assistant Professor Dept. of Botany and Plant Pathology 3082 Cordley Hall Oregon State University Corvallis, OR, 97331-2902, USA Ph.: +1-541-737-8471 Fax: +1-541-737-3573 Web: www.gramene.org www.plantontology.org From eelco.meuter at wur.nl Mon Nov 16 04:42:01 2009 From: eelco.meuter at wur.nl (Eelco Meuter) Date: Mon, 16 Nov 2009 10:42:01 +0100 Subject: [Po-dev] owl file Message-ID: <89DAD37A-E870-4E2D-880E-38ACAE133460@wur.nl> Dear Sire, Madam, Unfortunately, I failed to download the OWL file. Could you please send me a copy? If the copy is too large to send as attachment, you can use the service sendit.wur.nl to send large files. Thank you in advance. Kind regards, Eelco Meuter ----------------- Plant Production Systems Group, Wageningen University Droevendaalsesteeg 1, 6708 PB Wageningen P.O. Box 430, 6700 AK Wageningen The Netherlands http://www.pps.wur.nl This e-mail is for the intended addressee(s) only. The message and its attachments, if any, may contain confidential information. Use by an unintended addressee, by third parties or publication without permission of the sender is not allowed. If you have received the e-mail by mistake, please notify the sender and delete the e-mail and any attachments. We also inform you that agreements can only be entered into by authorised persons. From elserj at science.oregonstate.edu Mon Nov 16 17:34:54 2009 From: elserj at science.oregonstate.edu (Justin Elser) Date: Mon, 16 Nov 2009 14:34:54 -0800 Subject: [Po-dev] owl file In-Reply-To: <89DAD37A-E870-4E2D-880E-38ACAE133460@wur.nl> References: <89DAD37A-E870-4E2D-880E-38ACAE133460@wur.nl> Message-ID: <4B01D38E.5080405@science.oregonstate.edu> Could you please give me more information as to where you are downloading the file from? I did find that some of the obsolete files from gramene listed on the download page: http://plantontology.org/download/download.html were missing, so I fixed those, but I am unsure as to which file exactly you are trying to download. Can you please give me the page you are trying to download the file from, or the link you are using to download? Thanks, justin Eelco Meuter wrote: > Dear Sire, Madam, > > Unfortunately, I failed to download the OWL file. Could you please send me a copy? If the copy is too large to send as attachment, you can use the service sendit.wur.nl to send large files. > Thank you in advance. > > > Kind regards, > > Eelco Meuter > > > > ----------------- > Plant Production Systems Group, Wageningen University > Droevendaalsesteeg 1, 6708 PB Wageningen > P.O. Box 430, 6700 AK Wageningen > The Netherlands > > http://www.pps.wur.nl > > > This e-mail is for the intended addressee(s) only. The message and its attachments, if any, may contain confidential information. Use by an unintended addressee, by third parties or publication without permission of the sender is not allowed. If you have received the e-mail by mistake, please notify the sender and delete the e-mail and any attachments. > > We also inform you that agreements can only be entered into by authorised persons. > > > > > > > > > > > _______________________________________________ > Po-dev mailing list > Po-dev at plantontology.org > http://mail.plantontology.org/mailman/listinfo/po-dev > -- ********************************************************** * * * Justin Elser * * Computational Biology Post Doc * * Dept. of Botany and Plant Pathology * * Oregon State University * * * * email: elserj at science.oregonstate.edu * * internet: www.science.oregonstate.edu/~elserj * * * ********************************************************** From whetzel at stanford.edu Mon Nov 23 21:38:35 2009 From: whetzel at stanford.edu (Trish Whetzel) Date: Mon, 23 Nov 2009 18:38:35 -0800 Subject: [Po-dev] Plant ontologies Message-ID: <46381BB6-4E88-49A8-8400-03867EFA3949@stanford.edu> Dear PO developers, The BioPortal team is adding functionality to automatically load ontologies from SVN repositories. If you are interested in having your ontologies included in the automatic pull process, please fill-in the attached repository description file, the section from to following the examples provided. Best regards, Trish . Trish Whetzel, PhD Outreach Coordinator The National Center for Biomedical Ontology Ph: 650-721-2378 whetzel at stanford.edu http://www.bioontology.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ontology_repository.xml Type: text/xml Size: 1105 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: