From: Trish W. <wh...@pc...> - 2006-09-29 19:31:54
|
Hi Valerie, If I understand the question correctly, the MAGE class SeqFeature has an association to BioSequence which has 4 associations to OntologyEntry, one of which is called Type. The values for this were initially derived from the MGED Ontology (MO) BioSequenceType subclasses, but were deprecated in favor of using terms from the Sequence Ontology (SO). The mapping of MO to SO terms can be found at: http://song.sourceforge.net/so_mappings.shtml Trish > How does one discern what type of feature a MAGE SeqFeature is (gene, > binding site, etc.)? |
From: Valerie W. <val...@sr...> - 2006-09-29 19:41:28
|
Thanks, Trish, that's exactly what I was asking. Forgive my ignorance in this area, but can't a BioSequence have many different features associated with it? So are you saying that the BioSequence in question is only meant to have one type of SeqFeature associated with it? Valerie Trish Whetzel wrote: > Hi Valerie, > > If I understand the question correctly, the MAGE class SeqFeature has an > association to BioSequence which has 4 associations to OntologyEntry, one > of which is called Type. The values for this were initially derived from > the MGED Ontology (MO) BioSequenceType subclasses, but were > deprecated in favor of using terms from the Sequence Ontology (SO). The > mapping of MO to SO terms can be found at: > http://song.sourceforge.net/so_mappings.shtml > > Trish > > >> How does one discern what type of feature a MAGE SeqFeature is (gene, >> binding site, etc.)? > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Trish W. <wh...@pc...> - 2006-09-29 19:55:12
|
Hmm... yes I would think that a BioSequence could be annotated with more than one MO BioSequenceType term, however the UML model shows this with a cardinality of 1-1 so I think that limits the annotation to one type per BioSequence. I'll have to defer the reasoning for this (and how it is coded) to others more involved with the model development and generation of MAGE-ML. Trish > Forgive my ignorance in this area, but can't a BioSequence have many > different features associated with it? So are you saying that the > BioSequence in question is only meant to have one type of SeqFeature > associated with it? > > Valerie > > Trish Whetzel wrote: >> Hi Valerie, >> >> If I understand the question correctly, the MAGE class SeqFeature has an >> association to BioSequence which has 4 associations to OntologyEntry, one >> of which is called Type. The values for this were initially derived from >> the MGED Ontology (MO) BioSequenceType subclasses, but were deprecated in >> favor of using terms from the Sequence Ontology (SO). The mapping of MO to >> SO terms can be found at: >> http://song.sourceforge.net/so_mappings.shtml >> >> Trish >> >> >>> How does one discern what type of feature a MAGE SeqFeature is (gene, >>> binding site, etc.)? >> >> ------------------------------------------------------------------------- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to share >> your >> opinions on IT & business topics through brief surveys -- and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage > |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-29 20:45:40
|
Hi Trish and Valerie, SeqFeature is Describable so one can add a Description to it with text = =3D "FeatureType" and a URI to the appropriate documentation for that particular Feature then add the OntologyEntry using a SO term. But...in truth, when we designed MAGEv1 (and have pretty much carried this into FuGE and MAGEv2), to truly model annotating a Sequence was decided to be out of scope. Many users of MAGE form a pseudo-LSID identifier for their genes based on GenBank, RefSeq, Entrez, whatever, accession/identifiers then use that sequence database as the Database_ref. Later some other tool/software can come back and annotate the genes. But to add limited annotation, I think the above would work reasonably well. cheers, Michael > -----Original Message----- > From: mge...@li...=20 > [mailto:mge...@li...] On Behalf Of=20 > Valerie Wagner > Sent: Friday, September 29, 2006 12:41 PM > To: Trish Whetzel > Cc: mge...@li... > Subject: Re: [Mged-mage] How to tell SeqFeature type? >=20 >=20 > Thanks, Trish, that's exactly what I was asking. >=20 > Forgive my ignorance in this area, but can't a BioSequence have many=20 > different features associated with it? So are you saying that the=20 > BioSequence in question is only meant to have one type of SeqFeature=20 > associated with it? >=20 > Valerie >=20 > Trish Whetzel wrote: > > Hi Valerie, > >=20 > > If I understand the question correctly, the MAGE class=20 > SeqFeature has an=20 > > association to BioSequence which has 4 associations to=20 > OntologyEntry, one=20 > > of which is called Type. The values for this were initially=20 > derived from=20 > > the MGED Ontology (MO) BioSequenceType subclasses, but were=20 > > deprecated in favor of using terms from the Sequence=20 > Ontology (SO). The=20 > > mapping of MO to SO terms can be found at: > > http://song.sourceforge.net/so_mappings.shtml > >=20 > > Trish > >=20 > >=20 > >> How does one discern what type of feature a MAGE=20 > SeqFeature is (gene, > >> binding site, etc.)? > >=20 > >=20 > -------------------------------------------------------------- > ----------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the=20 > chance to share your > > opinions on IT & business topics through brief surveys --=20 > and earn cash > >=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge &CID=3DDEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage ------------------------------------------------------------------------ - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys -- and earn cash http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V _______________________________________________ Mged-mage mailing list Mge...@li... https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Valerie W. <val...@sr...> - 2006-09-29 20:51:07
|
I'm writing a loader for the BioWarehouse that takes MAGE-ML input. So for arbitrary input, it would be hard to parse an arbitrary description with any certainty of what might be in it. If it's the case that the BioSequence Type association determines the (single) type of SeqFeatures, then that's at least something I can parse. Are you saying that this BioSequence Type association doesn't actually tell us the types of the SeqFeatures because people can use Descriptions or identifiers to determine the type? (And in that case, what is meant by the BioSequence Type association?) thanks, Valerie Miller, Michael D (Rosetta) wrote: > Hi Trish and Valerie, > > SeqFeature is Describable so one can add a Description to it with text = > "FeatureType" and a URI to the appropriate documentation for that > particular Feature then add the OntologyEntry using a SO term. > > But...in truth, when we designed MAGEv1 (and have pretty much carried > this into FuGE and MAGEv2), to truly model annotating a Sequence was > decided to be out of scope. Many users of MAGE form a pseudo-LSID > identifier for their genes based on GenBank, RefSeq, Entrez, whatever, > accession/identifiers then use that sequence database as the > Database_ref. Later some other tool/software can come back and annotate > the genes. > > But to add limited annotation, I think the above would work reasonably > well. > > cheers, > Michael > >> -----Original Message----- >> From: mge...@li... >> [mailto:mge...@li...] On Behalf Of >> Valerie Wagner >> Sent: Friday, September 29, 2006 12:41 PM >> To: Trish Whetzel >> Cc: mge...@li... >> Subject: Re: [Mged-mage] How to tell SeqFeature type? >> >> >> Thanks, Trish, that's exactly what I was asking. >> >> Forgive my ignorance in this area, but can't a BioSequence have many >> different features associated with it? So are you saying that the >> BioSequence in question is only meant to have one type of SeqFeature >> associated with it? >> >> Valerie >> >> Trish Whetzel wrote: >>> Hi Valerie, >>> >>> If I understand the question correctly, the MAGE class >> SeqFeature has an >>> association to BioSequence which has 4 associations to >> OntologyEntry, one >>> of which is called Type. The values for this were initially >> derived from >>> the MGED Ontology (MO) BioSequenceType subclasses, but were >>> deprecated in favor of using terms from the Sequence >> Ontology (SO). The >>> mapping of MO to SO terms can be found at: >>> http://song.sourceforge.net/so_mappings.shtml >>> >>> Trish >>> >>> >>>> How does one discern what type of feature a MAGE >> SeqFeature is (gene, >>>> binding site, etc.)? >>> >> -------------------------------------------------------------- >> ----------- >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the >> chance to share your >>> opinions on IT & business topics through brief surveys -- >> and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge > &CID=DEVDEV >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage > > > ------------------------------------------------------------------------ > - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE > V > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage > > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Miller, M. D (Rosetta) <Michael_Miller@Rosettabio.com> - 2006-09-29 21:03:09
|
Hi Valerie, it is intended for a higher level type (from the documentation): "type: The type of biosequence, i.e. gene, exon, UniGene cluster,=20 fragment, BAC, EST, etc." > Are you saying that this BioSequence Type association doesn't=20 > actually=20 > tell us the types of the SeqFeatures because people can use=20 > Descriptions=20 > or identifiers to determine the type? (And in that case,=20 > what is meant=20 > by the BioSequence Type association?) I really wasn't saying anything more than I was saying. > So=20 > for arbitrary input, it would be hard to parse an arbitrary=20 > description=20 > with any certainty of what might be in it. I've seen very few applications use SeqFeature--as an importer/consumer without knowledge of the source, one can only provide a place to hold what's in the MAGE elements/objects. How does an importer actually know much about the BioSequence itself? My suggestion was (apparently wrongly) more geared towards an exporter or in-house application. cheers, Michael > -----Original Message----- > From: Valerie Wagner [mailto:val...@sr...]=20 > Sent: Friday, September 29, 2006 1:51 PM > To: Miller, Michael D (Rosetta) > Cc: Trish Whetzel; mge...@li... > Subject: Re: [Mged-mage] How to tell SeqFeature type? >=20 >=20 > I'm writing a loader for the BioWarehouse that takes MAGE-ML=20 > input. So=20 > for arbitrary input, it would be hard to parse an arbitrary=20 > description=20 > with any certainty of what might be in it. If it's the case that the=20 > BioSequence Type association determines the (single) type of=20 > SeqFeatures, then that's at least something I can parse. >=20 > Are you saying that this BioSequence Type association doesn't=20 > actually=20 > tell us the types of the SeqFeatures because people can use=20 > Descriptions=20 > or identifiers to determine the type? (And in that case,=20 > what is meant=20 > by the BioSequence Type association?) >=20 > thanks, > Valerie >=20 > Miller, Michael D (Rosetta) wrote: > > Hi Trish and Valerie, > >=20 > > SeqFeature is Describable so one can add a Description to=20 > it with text =3D > > "FeatureType" and a URI to the appropriate documentation for that > > particular Feature then add the OntologyEntry using a SO term. > >=20 > > But...in truth, when we designed MAGEv1 (and have pretty=20 > much carried > > this into FuGE and MAGEv2), to truly model annotating a Sequence was > > decided to be out of scope. Many users of MAGE form a pseudo-LSID > > identifier for their genes based on GenBank, RefSeq,=20 > Entrez, whatever, > > accession/identifiers then use that sequence database as the > > Database_ref. Later some other tool/software can come back=20 > and annotate > > the genes. > >=20 > > But to add limited annotation, I think the above would work=20 > reasonably > > well. > >=20 > > cheers, > > Michael > >=20 > >> -----Original Message----- > >> From: mge...@li...=20 > >> [mailto:mge...@li...] On Behalf Of=20 > >> Valerie Wagner > >> Sent: Friday, September 29, 2006 12:41 PM > >> To: Trish Whetzel > >> Cc: mge...@li... > >> Subject: Re: [Mged-mage] How to tell SeqFeature type? > >> > >> > >> Thanks, Trish, that's exactly what I was asking. > >> > >> Forgive my ignorance in this area, but can't a BioSequence=20 > have many=20 > >> different features associated with it? So are you saying that the=20 > >> BioSequence in question is only meant to have one type of=20 > SeqFeature=20 > >> associated with it? > >> > >> Valerie > >> > >> Trish Whetzel wrote: > >>> Hi Valerie, > >>> > >>> If I understand the question correctly, the MAGE class=20 > >> SeqFeature has an=20 > >>> association to BioSequence which has 4 associations to=20 > >> OntologyEntry, one=20 > >>> of which is called Type. The values for this were initially=20 > >> derived from=20 > >>> the MGED Ontology (MO) BioSequenceType subclasses, but were=20 > >>> deprecated in favor of using terms from the Sequence=20 > >> Ontology (SO). The=20 > >>> mapping of MO to SO terms can be found at: > >>> http://song.sourceforge.net/so_mappings.shtml > >>> > >>> Trish > >>> > >>> > >>>> How does one discern what type of feature a MAGE=20 > >> SeqFeature is (gene, > >>>> binding site, etc.)? > >>> > >> -------------------------------------------------------------- > >> ----------- > >>> Take Surveys. Earn Cash. Influence the Future of IT > >>> Join SourceForge.net's Techsay panel and you'll get the=20 > >> chance to share your > >>> opinions on IT & business topics through brief surveys --=20 > >> and earn cash > >> http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge > > &CID=3DDEVDEV > >> _______________________________________________ > >> Mged-mage mailing list > >> Mge...@li... > >> https://lists.sourceforge.net/lists/listinfo/mged-mage > >=20 > >=20 > >=20 > -------------------------------------------------------------- > ---------- > > - > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the=20 > chance to share > > your > > opinions on IT & business topics through brief surveys --=20 > and earn cash > >=20 > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge &CID=3DDEVDE > V > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage >=20 >=20 >=20 > ------------------------------------------------------------------------ - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys -- and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3D= DEVDE V > _______________________________________________ > Mged-mage mailing list > Mge...@li... > https://lists.sourceforge.net/lists/listinfo/mged-mage |
From: Valerie W. <val...@sr...> - 2006-09-29 21:06:30
|
Fair enough--thanks for your assistance! cheers, Valerie Miller, Michael D (Rosetta) wrote: > Hi Valerie, > > it is intended for a higher level type (from the documentation): > > "type: The type of biosequence, i.e. gene, exon, UniGene cluster, > fragment, BAC, EST, etc." > >> Are you saying that this BioSequence Type association doesn't >> actually >> tell us the types of the SeqFeatures because people can use >> Descriptions >> or identifiers to determine the type? (And in that case, >> what is meant >> by the BioSequence Type association?) > > I really wasn't saying anything more than I was saying. > >> So >> for arbitrary input, it would be hard to parse an arbitrary >> description >> with any certainty of what might be in it. > > I've seen very few applications use SeqFeature--as an importer/consumer > without knowledge of the source, one can only provide a place to hold > what's in the MAGE elements/objects. How does an importer actually know > much about the BioSequence itself? > > My suggestion was (apparently wrongly) more geared towards an exporter > or in-house application. > > cheers, > Michael > >> -----Original Message----- >> From: Valerie Wagner [mailto:val...@sr...] >> Sent: Friday, September 29, 2006 1:51 PM >> To: Miller, Michael D (Rosetta) >> Cc: Trish Whetzel; mge...@li... >> Subject: Re: [Mged-mage] How to tell SeqFeature type? >> >> >> I'm writing a loader for the BioWarehouse that takes MAGE-ML >> input. So >> for arbitrary input, it would be hard to parse an arbitrary >> description >> with any certainty of what might be in it. If it's the case that the >> BioSequence Type association determines the (single) type of >> SeqFeatures, then that's at least something I can parse. >> >> Are you saying that this BioSequence Type association doesn't >> actually >> tell us the types of the SeqFeatures because people can use >> Descriptions >> or identifiers to determine the type? (And in that case, >> what is meant >> by the BioSequence Type association?) >> >> thanks, >> Valerie >> >> Miller, Michael D (Rosetta) wrote: >>> Hi Trish and Valerie, >>> >>> SeqFeature is Describable so one can add a Description to >> it with text = >>> "FeatureType" and a URI to the appropriate documentation for that >>> particular Feature then add the OntologyEntry using a SO term. >>> >>> But...in truth, when we designed MAGEv1 (and have pretty >> much carried >>> this into FuGE and MAGEv2), to truly model annotating a Sequence was >>> decided to be out of scope. Many users of MAGE form a pseudo-LSID >>> identifier for their genes based on GenBank, RefSeq, >> Entrez, whatever, >>> accession/identifiers then use that sequence database as the >>> Database_ref. Later some other tool/software can come back >> and annotate >>> the genes. >>> >>> But to add limited annotation, I think the above would work >> reasonably >>> well. >>> >>> cheers, >>> Michael >>> >>>> -----Original Message----- >>>> From: mge...@li... >>>> [mailto:mge...@li...] On Behalf Of >>>> Valerie Wagner >>>> Sent: Friday, September 29, 2006 12:41 PM >>>> To: Trish Whetzel >>>> Cc: mge...@li... >>>> Subject: Re: [Mged-mage] How to tell SeqFeature type? >>>> >>>> >>>> Thanks, Trish, that's exactly what I was asking. >>>> >>>> Forgive my ignorance in this area, but can't a BioSequence >> have many >>>> different features associated with it? So are you saying that the >>>> BioSequence in question is only meant to have one type of >> SeqFeature >>>> associated with it? >>>> >>>> Valerie >>>> >>>> Trish Whetzel wrote: >>>>> Hi Valerie, >>>>> >>>>> If I understand the question correctly, the MAGE class >>>> SeqFeature has an >>>>> association to BioSequence which has 4 associations to >>>> OntologyEntry, one >>>>> of which is called Type. The values for this were initially >>>> derived from >>>>> the MGED Ontology (MO) BioSequenceType subclasses, but were >>>>> deprecated in favor of using terms from the Sequence >>>> Ontology (SO). The >>>>> mapping of MO to SO terms can be found at: >>>>> http://song.sourceforge.net/so_mappings.shtml >>>>> >>>>> Trish >>>>> >>>>> >>>>>> How does one discern what type of feature a MAGE >>>> SeqFeature is (gene, >>>>>> binding site, etc.)? >>>> -------------------------------------------------------------- >>>> ----------- >>>>> Take Surveys. Earn Cash. Influence the Future of IT >>>>> Join SourceForge.net's Techsay panel and you'll get the >>>> chance to share your >>>>> opinions on IT & business topics through brief surveys -- >>>> and earn cash >>>> http://www.techsay.com/default.php?page=join.php&p=sourceforge >>> &CID=DEVDEV >>>> _______________________________________________ >>>> Mged-mage mailing list >>>> Mge...@li... >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>> >>> >> -------------------------------------------------------------- >> ---------- >>> - >>> Take Surveys. Earn Cash. Influence the Future of IT >>> Join SourceForge.net's Techsay panel and you'll get the >> chance to share >>> your >>> opinions on IT & business topics through brief surveys -- >> and earn cash >> http://www.techsay.com/default.php?page=join.php&p=sourceforge > &CID=DEVDE >> V >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> >> >> >> > ------------------------------------------------------------------------ > - >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to > share your >> opinions on IT & business topics through brief surveys -- and earn > cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE > V >> _______________________________________________ >> Mged-mage mailing list >> Mge...@li... >> https://lists.sourceforge.net/lists/listinfo/mged-mage > > > |