microarray-ontol-digest Monday, December 17 2001 Volume 01 : Number 016 ---------------------------------------------------------------------- Date: Fri, 7 Dec 2001 19:19:59 -0500 (EST) From: Chris Stoeckert Subject: [microarray-ontol] Genotype to Phenotype Ontology Workshop Date: Fri, 07 Dec 2001 10:27:14 +0000 To: microarray-ontol@ebi.ac.uk From: Robert Stevens Subject: Genotype to Phenotype Ontology Workshop Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Genotype To Phenotype: Linking Bioinformatics and Medical Informatics Ontologies Call For Submission and Participation A one-day workshop on ">From Genotype to Phenotype Linking Bioinformatics and Medical Informatics Ontologies" (Chaired by Alan Rector and Robert Stevens) is being held as part of Manchester Bioinformatics Week - Easter 2002. The details on the workshop may be found at http://www.biomed2.man.ac.uk/bioinfconferen/default.htm The medical informatics community has had an interest and a wealth of experience in developing and using ontologies, that stretches back over many decades. The younger Bioinformatics community has also indicated a growing interest in the subject area. There is both a common interest and a diversity in these fields, that together, we hope can be of mutual interest and benefit to both communities. Bioinformatics ontologies have described knowledge of the genotype of organisms: Their molecular biology, function, pathways, molecular structures and general classifications. Medical informatics ontologies have described knowledge about phenotype: Appearance, anatomy, disease, etc. of mainly one organism -- Human, but occaisionally others. the genotype is the genes and genetics, together with associated cellular machinery, that gives rise to those phenotypes. As Bioinformatics gears up to manage, store and analyse data and knowledge from new experimental techniques, such as micro array gene expression, the discipline is becoming more interested in linking knowledge of genotype to the phenotype governed by that gene expression -- or more broadly in linking molecular - genetic, genomic and proteomic - mechanisms to their consequences for physiology and pathology and ultimately clinical medicine - i.e. the health and disease of organs and organisms. Making this linkage is a key step in understanding the mechanisms of known drugs and discovering new ones. The linking of genotype and phenotype ontologies offers interesting opportunities for collaboration between Medical Informatics and Bioinformatics. I hope that you will be able to attend and I also hope that you can submit an abstract to the workshop. Registration and Submission of Abstracts is possible via the web site. The deadline for receipt of abstracts is 25th January 2002. There are reduced fees for payments received before this date. ------------------------------ Date: 09 Dec 2001 14:31:49 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: [microarray-ontol] MAGE ontologies Hey Chris, So it seems that you and Paul had a lengthy talk about the conjoining of MAGE with the growing MGED ontologies. It seems that the biggest issue is how to roll the heavily object oriented ontology that is being produced with my the lighter weight model that we built into MAGE. * Where are conflicting (if anywhere)? * What pieces are missing from MAGE to support the richer semantics possible with ontological objects? * How can these richer ontologies coexist with simpler ones such as simple restricted vocabs. Cheers, jas. ------------------------------ Date: 09 Dec 2001 14:33:12 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: [microarray-ontol] MAGE ontology list Hey All, Here is the list of all OntologyEntries that exist in MAGE, categorized by how complex I think they will be to create. There are only two that I think will take much effort, and you're already working on the big one. jas. - -- Finished: ========= BioSequence:Species DesignElementGroup:Species Trivial: List ============= Image:Format {TIFF,JPG} BioSequence:PolymerType {DNA,RNA,protein} NodeValue:DataType {float,int,string} Parameter:DataType {float,int,string} QuantitationType:DataType {float,int,string} NodeValue:Scale {log_2,log_10} QuantitationType:Scale {log_2,log_10} OpenEnded: List ============= Contact:Roles {experiment_provider,software_provider} BioSequence:OntologyEntries Reporter:FailTypes Reporter:WarningTypes DesignElement:ControlType Description:Annotations Medium: List ============= DerivedBioAssay:Type {replicate_average} PhysicalArrayDesign:SurfaceType ArrayGroup:SubstrateType BioSequence:Type {exon,intron,gene} DesignElementGroup:Type BioMaterial:MaterialType BioSample:Type DatabaseEntry:Type BibliographicReference:Parameters {publisher_address} ExperimentDesign:Types {heat_shock,osmotic_shock,time_series} ExperimentalFactor:Category {biological_factor,methodological_factor} Protocol:Type {cDNA_labelling,RNA_extraction} Hardware:Type {two_color_scanner,ceramic_pin_arrayer,computer,thermocycler} Software:Type {feature_extraction,spot_finding} Compound:MerckIndex => Compound:Indices {Merck,CAS} Hard: DAG ========= Treatment:Action {wait,centrifuge,add} Impossible: Object ================== BioSource:Characteristics ------------------------------ Date: Mon, 10 Dec 2001 12:25:57 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] MAGE ontology list Hey Jason, Many thanks for this. While the main focus will continue to be on BiomaterialDescriptions, I think we are now at the point where we can also start thinking about these as well. I have some questions about your list. Is the syntax: Class:Attribute{one-of}? What does Species mean in the context of BioSequence and DesignElementGroup? More generally, are there definitions for these? I think generating these would be the next step. I will respond to your other mail about going from the microarray ontology to MAGE later in the week as that will take a bit of thought to answer clearly. Cheers, Chris On Sunday, December 9, 2001, at 04:33 PM, Jason E. Stewart wrote: > Hey All, > > Here is the list of all OntologyEntries that exist in MAGE, > categorized by how complex I think they will be to create. There are > only two that I think will take much effort, and you're already > working on the big one. > > jas. > > -- > Finished: > ========= > BioSequence:Species > DesignElementGroup:Species > > Trivial: List > ============= > Image:Format {TIFF,JPG} > BioSequence:PolymerType {DNA,RNA,protein} > NodeValue:DataType {float,int,string} > Parameter:DataType {float,int,string} > QuantitationType:DataType {float,int,string} > NodeValue:Scale {log_2,log_10} > QuantitationType:Scale {log_2,log_10} > > OpenEnded: List > ============= > Contact:Roles {experiment_provider,software_provider} > BioSequence:OntologyEntries > Reporter:FailTypes > Reporter:WarningTypes > DesignElement:ControlType > Description:Annotations > > Medium: List > ============= > DerivedBioAssay:Type {replicate_average} > PhysicalArrayDesign:SurfaceType > ArrayGroup:SubstrateType > BioSequence:Type {exon,intron,gene} > DesignElementGroup:Type > BioMaterial:MaterialType > BioSample:Type > DatabaseEntry:Type > BibliographicReference:Parameters {publisher_address} > ExperimentDesign:Types {heat_shock,osmotic_shock,time_series} > ExperimentalFactor:Category {biological_factor,methodological_factor} > Protocol:Type {cDNA_labelling,RNA_extraction} > Hardware:Type > {two_color_scanner,ceramic_pin_arrayer,computer,thermocycler} > Software:Type {feature_extraction,spot_finding} > Compound:MerckIndex => Compound:Indices {Merck,CAS} > > Hard: DAG > ========= > Treatment:Action {wait,centrifuge,add} > > Impossible: Object > ================== > BioSource:Characteristics > ------------------------------ Date: 10 Dec 2001 10:43:52 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] MAGE ontology list "Chris Stoeckert" writes: > Is the syntax: Class:Attribute{one-of}? What does Species mean in > the context of BioSequence and DesignElementGroup? It is Class:Attribute {example1,example2, ... } The examples are definately not exclusive, they are just my minimal effort to provide some basic context. > More generally, are there definitions for these? I think generating > these would be the next step. The definitions are all in the model. I can extract these very simply from the model. I'll publish these later today. jas. ------------------------------ Date: Tue, 11 Dec 2001 14:05:21 +0000 From: Helen Parkinson Subject: [microarray-ontol] Ontology workshop in Manchester, UK Posted on behalf of Robert Stevens: robert.stevens@cs.man.ac.uk, please foward to anyone who might be interested, thanks Helen - --------------------------------------------------------------------- Genotype to Phenotype: Linking Bioinformatics and medical Informatics Ontologies Part of Manchester Bioinformatics Week Easter 2002 A one-day workshop on ">From Genotype to Phenotype Linking Bioinformatics and Medical Informatics Ontologies" (Chaired by Alan Rector and Robert Stevens) is being held as part of Manchester Bioinformatics Week - Easter 2002. The details on the workshop may be found at http://www.biomed2.man.ac.uk/bioinfconferen/default.htm The medical informatics community has had an interest and a wealth of experience in developing and using ontologies, that stretches back over many decades. The younger Bioinformatics community has also indicated a growing interest in the subject area. There is both a common interest and a diversity in these fields, that together, we hope can be of mutual interest and benefit to both communities. Bioinformatics ontologies have described knowledge of the genotype of organisms: Their molecular biology, function, pathways, molecular structures and general classifications. Medical informatics ontologies have described knowledge about phenotype: Appearance, anatomy, disease, etc. of mainly one organism -- Human, but occaisionally others. the genotype is the genes and genetics, together with associated cellular machinery, that gives rise to those phenotypes. As Bioinformatics gears up to manage, store and analyse data and knowledge from new experimental techniques, such as micro array gene expression, the discipline is becoming more interested in linking knowledge of genotype to the phenotype governed by that gene expression -- or more broadly in linking molecular - genetic, genomic and proteomic - mechanisms to their consequences for physiology and pathology and ultimately clinical medicine - i.e. the health and disease of organs and organisms. Making this linkage is a key step in understanding the mechanisms of known drugs and discovering new ones. The linking of genotype and phenotype ontologies offers interesting opportunities for collaboration between Medical Informatics and Bioinformatics. I hope that you will be able to attend and I also hope that you can submit an abstract to the workshop. Registration and Submission of Abstracts is possible via the web site. The deadline for receipt of abstracts is 25th January 2002. There are reduced fees for payments received before this date. ------------------------------ Date: Wed, 12 Dec 2001 08:39:13 +0000 (GMT) From: Alvis Brazma Subject: [microarray-ontol] MGED 4 This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. - --=_64394002.B7D69F5E Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Content-ID: REGISTRATION OPEN! MGED 4 February 13-16, 2002 Hynes Convention Center Boston, MA Registration deadline, January 21, 2002 Online registration, abstract submission, and hotel reservation are now available for the MGED 4 meeting at http://php.aaas.org/mged This year MGED is meeting in association with the AAAS Annual Meeting and Science Innovation Exposition (to be held February 14-19 in the same location). Because of this there are several things new about the meeting. 1. REGISTRATION: The registration fee is $260 for all classes of registrants. There is not a lower rate for students or a higher rate for industry. Just one rate! To register for MGED you MUST use the MGED Registration form at http://php.aaas.org/mged. Please note that those registering after January 21 must do so on-site and at a higher rate. With your MGED registration you will receive a complimentary registration to all seminars, symposia, lectures, and events of the AAAS meeting. Please be aware that your registration does NOT include housing or meals. 2. ABSTRACTS: You should submit an abstract ONLY if you have been invited to speak or if you wish to present a poster. Attendees to MGED not speaking or presenting a poster are not asked to submit an abstract. 3. HOUSING: Because we are meeting with AAAS, housing arrangements for the meeting are those for the larger AAAS Meeting. You may make your hotel reservation through the AAAS Housing Bureau at http://www.aaasmeeting.org/Info.shtml AAAS has special negotiated rates with its hotels that are available only through the AAAS Housing Bureau. If you wish to seek other accommodations, you may consult web and other resources for alternate hotels. 4. TRAVEL: AAAS has negotiated rates for air travel. Fares now are low so make your reservations soon! http://www.aaasmeeting.org/Info.shtml 5. AGENDA: See http://php.aaas.org/mged for a current agenda for MGED 4 6. 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AAAAAAAAAA== - --=_64394002.B7D69F5E-- ------------------------------ Date: Wed, 12 Dec 2001 14:31:49 -0500 From: Chris Stoeckert Subject: [microarray-ontol] Re: Hi Paul, I think your proposal to associate NameValueType and OntologyEntry to OntologyEntry should work nicely. Note that what MAGE calls Characteristics (an association/attribute of BioSource) is what our ontology calls BiosourceProperty (a class which is a subclass of BiomaterialDescription). Promoting Characteristics to Biomaterials should work. This means that LabeledExtract and BioSample also have Characteristics (i.e., associations to OntologyEntry) now and BioSampleType association is redundant. Note that in our ontology we have separated LabeledExtract, Biosample, and Biosource as subclasses of BiomaterialState which like BiosourceProperty is a subclass of BiomaterialDescription (root). Chris On Friday, December 7, 2001, at 05:06 AM, PTSpellman@lbl.gov wrote: > All, > > Chris Stoeckert and I had a conversation yesterday about MAGE > ontologies and at long last I was convinced that some modifications in > the biomaterial package need to be made. > > Specifically: > BioSource:Characteristics will be much more powerful if OntologyEntry > can effectively become an instantiation of a class in an Ontology (we > all know that Objects are more powerful than hierarchies). To do this > OntologyEntry needs the ability to have attributes and daughter > classes. I propose to solve this by allowing associations to NVT and > OE, this effectively allows OE's to contain the information that > objects have. > > Also, BioMaterials at present have no way of inheiriting from > BioSources that have different characteristics. One easy way to solve > this is to move the Characteristics from BioSource to BioMaterial. A > good example is if you were doing a stress test on a mice and you first > put it in a large cage and then put it in a small cage. Another > example is if during the experiment a mutation occured that change the > organisms genotype. A more complex, and potentially better method > would be to add characteristics to treatment so that you could have an > action change and or measure that alters these parameters. > > I have attached the BioMaterial png (unmodified) for reference. > > Paul > > > > Add to MAGE > > Attributes 0..* > OntologyEntry ------------> NamedValueType > > Characteristics 0..* > OntologyEntry -------------------> OntologyEntry > > Characteristics 0..* > Treatment -----------------> OntologyEntry > > ------------------------------ Date: Wed, 12 Dec 2001 14:56:51 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] MAGE ontologies Hey Jason, I think the associations that Paul Spellman proposed (I just sent mail out responding to it) should help a lot. Essentially, we need to look at whether every ontology object has a comparable MAGE object. Some of these will be explicit such as Treatment and Compound. I think others will now be implicit in OntologyEntry which can be used to build Ontology objects with the new associations Paul has proposed (NameValueType, OntologyEntry). Will start this process of mapping Ontology objects to MAGE objects and encourage others to join in. Cheers, Chris On Sunday, December 9, 2001, at 04:31 PM, Jason E. Stewart wrote: > Hey Chris, > > So it seems that you and Paul had a lengthy talk about the conjoining > of MAGE with the growing MGED ontologies. It seems that the biggest > issue is how to roll the heavily object oriented ontology that is > being produced with my the lighter weight model that we built into > MAGE. > > * Where are conflicting (if anywhere)? > * What pieces are missing from MAGE to support the richer semantics > possible with ontological objects? > * How can these richer ontologies coexist with simpler ones such as > simple restricted vocabs. > > Cheers, > jas. > ------------------------------ Date: Wed, 12 Dec 2001 17:10:39 -0500 From: Chris Stoeckert Subject: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Begin forwarded message: > From: "Miller, Michael" > Date: Wed Dec 12, 2001 03:42:46 PM US/Eastern > To: "'Chris Stoeckert'" , > PTSpellman@lbl.gov > Cc: mged-mage@lists.sourceforge.net, microarray-ontol@ebi.ac.uk, > "'LSR-GE'" > Subject: RE: [Mged-mage] Re:OntologyEntry changes > > Chris and Paul, > > I believe I understand the issue and solution here and I'm in agreement. > > OntologyEntry already has an association to NVT by way of being > extendable, > but this proposed NVT attribute association is more specific and would > be > part of the formal annotation. > > I'm currently in the middle of putting together the issues people have > raised over the last few months. Since we are scattered across the > world, > we'll need some sort of process to decide what goes into v1.0, what is > defered to v2.0, what appeared to be an issue but isn't (because people > agree it has to be the way it is) and issues that are good points but > can be > lived with. > > Once the OMG approves the standard as an official specification, they > provide good support for recording and voting for issues but until > then, for > the changes that will go in the submittal on Jan. 7th, I'm willing to > curate > the issues, but we need either through teleconference or email to have > a way > to come to consensus. (I know I'm harping on this point but as editor > of > the submittal I need guidance) > > This issue, by the way, I think should go into the next submittal. It > is > also the type of change that the OMG would think appropriate after it's > an > adopted specification in the finalization phase before it becomes > available > (hopefully from February to June) so there will be a chance to make > further > changes. > > thanks, > Michael > >> -----Original Message----- >> From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] >> Sent: Wednesday, December 12, 2001 11:32 AM >> To: PTSpellman@lbl.gov >> Cc: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk >> Subject: [Mged-mage] Re: >> >> >> Hi Paul, >> I think your proposal to associate NameValueType and OntologyEntry to >> OntologyEntry should work nicely. >> Note that what MAGE calls Characteristics (an >> association/attribute of >> BioSource) is what our ontology calls BiosourceProperty (a >> class which >> is a subclass of BiomaterialDescription). >> Promoting Characteristics to Biomaterials should work. This >> means that >> LabeledExtract and BioSample also have Characteristics (i.e., >> associations to OntologyEntry) now and BioSampleType association is >> redundant. Note that in our ontology we have separated >> LabeledExtract, >> Biosample, and Biosource as subclasses of BiomaterialState which like >> BiosourceProperty is a subclass of BiomaterialDescription (root). >> >> Chris >> >> On Friday, December 7, 2001, at 05:06 AM, PTSpellman@lbl.gov wrote: >> >>> All, >>> >>> Chris Stoeckert and I had a conversation yesterday about MAGE >>> ontologies and at long last I was convinced that some >> modifications in >>> the biomaterial package need to be made. >>> >>> Specifically: >>> BioSource:Characteristics will be much more powerful if >> OntologyEntry >>> can effectively become an instantiation of a class in an >> Ontology (we >>> all know that Objects are more powerful than hierarchies). >> To do this >>> OntologyEntry needs the ability to have attributes and daughter >>> classes. I propose to solve this by allowing associations >> to NVT and >>> OE, this effectively allows OE's to contain the information that >>> objects have. >>> >>> Also, BioMaterials at present have no way of inheiriting from >>> BioSources that have different characteristics. One easy >> way to solve >>> this is to move the Characteristics from BioSource to >> BioMaterial. A >>> good example is if you were doing a stress test on a mice >> and you first >>> put it in a large cage and then put it in a small cage. Another >>> example is if during the experiment a mutation occured that >> change the >>> organisms genotype. A more complex, and potentially better method >>> would be to add characteristics to treatment so that you >> could have an >>> action change and or measure that alters these parameters. >>> >>> I have attached the BioMaterial png (unmodified) for reference. >>> >>> Paul >>> >>> >>> >>> Add to MAGE >>> >>> Attributes 0..* >>> OntologyEntry ------------> NamedValueType >>> >>> Characteristics 0..* >>> OntologyEntry -------------------> OntologyEntry >>> >>> Characteristics 0..* >>> Treatment -----------------> OntologyEntry >>> >>> >> >> >> _______________________________________________ >> Mged-mage mailing list >> Mged-mage@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/mged-mage >> > > _______________________________________________ > Mged-mage mailing list > Mged-mage@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mged-mage > ------------------------------ Date: 13 Dec 2001 13:57:54 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Hey All, I second Michael's continued request to have a submitters conference call to go over all proposed changes to the Model (including those 'proposals' that I've already committed to CVS ;-). I agree that moving Characteristics from BioSource to BioMaterial is a good one, that was an oversight. I agree that there is confusion between the role of BioMaterial:materialType, and BioSample:type. I'm afraid I'm not clear on the reasons why we need to make the MAGE model of OntologyEntry more rich than it currently is, I'm not opposed to such a plan, just that I've not been part of the discussion. The little I know is that Chris is creating a rich ontology for BioSource:characteristics using an Object based ontology as opposed to a simple list based controlled vocabulary. The MAGE OntologyEntry was designed primarily to capture controlled vocabularies, or tree based ontologies. My naive reply would be that for the description of the GE data, we don't need to capture any more, because the detailed ontology information (attributes and characteristics and sub-classes and super-classes) is already captured someplace else. For example, when annotating sequences with GO ID's, one doesn't need to store any inheritance relationships for any given ID, because it's all stored in the GO database. All you need to know is the ID, right? If you want to conduct an detailed analysis of all genes that have a specific molecular function, you will need to combine your analysis with the GO DB. Likewise, in my navie thinking all we to store for an MGED OntologyEntry is it's unique ID. My concern about the discussion that I'm seeing is that it is proposing to build an object model for ontologies which is beyond the scope of this work. I want to encourage the MGED ontology to be rich, and I want to ensure that we support it's use in MAGE, but I want to make sure that we separate the needs for *building* an ontology from the needs of *using* that ontology. As I say, this is a rather naive perspective on my part, and if Chris or Paul could help educate me as to why we need to capture something more than: * What ontology the entry comes from (GO, MGED, etc) * What the entries unique ID is I would be grateful. In my view, the existing attributes, 'identifier' and 'name' (via Identifiable), 'description', 'value', and 'category' should be sufficient level of detail for the needs of MAGE-OM. If Chris or Paul have ideas as to how they would be used that can't be handled using those attributes, that would simplify the discussion. Cheers, jas. "Chris Stoeckert" writes: > Begin forwarded message: > > > From: "Miller, Michael" > > Date: Wed Dec 12, 2001 03:42:46 PM US/Eastern > > To: "'Chris Stoeckert'" , > > PTSpellman@lbl.gov > > > Cc: mged-mage@lists.sourceforge.net, microarray-ontol@ebi.ac.uk, > > "'LSR-GE'" > > > Subject: RE: [Mged-mage] Re:OntologyEntry changes > > > > Chris and Paul, > > > > I believe I understand the issue and solution here and I'm in agreement. > > > > OntologyEntry already has an association to NVT by way of being > > extendable, > > > but this proposed NVT attribute association is more specific and > > would be > > > part of the formal annotation. > > > > I'm currently in the middle of putting together the issues people have > > raised over the last few months. Since we are scattered across the > > world, > > > we'll need some sort of process to decide what goes into v1.0, what is > > defered to v2.0, what appeared to be an issue but isn't (because people > > agree it has to be the way it is) and issues that are good points > > but can be > > > lived with. > > > > Once the OMG approves the standard as an official specification, they > > provide good support for recording and voting for issues but until > > then, for > > > the changes that will go in the submittal on Jan. 7th, I'm willing > > to curate > > > the issues, but we need either through teleconference or email to > > have a way > > > to come to consensus. (I know I'm harping on this point but as > > editor of > > > the submittal I need guidance) > > > > This issue, by the way, I think should go into the next submittal. > > It is > > > also the type of change that the OMG would think appropriate after > > it's an > > > adopted specification in the finalization phase before it becomes > > available > > > (hopefully from February to June) so there will be a chance to make > > further > > > changes. > > > > thanks, > > Michael > > > >> -----Original Message----- > >> From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] > >> Sent: Wednesday, December 12, 2001 11:32 AM > >> To: PTSpellman@lbl.gov > >> Cc: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk > >> Subject: [Mged-mage] Re: > >> > >> > >> Hi Paul, > >> I think your proposal to associate NameValueType and OntologyEntry to > >> OntologyEntry should work nicely. > >> Note that what MAGE calls Characteristics (an > >> association/attribute of > >> BioSource) is what our ontology calls BiosourceProperty (a > >> class which > >> is a subclass of BiomaterialDescription). > >> Promoting Characteristics to Biomaterials should work. This > >> means that > >> LabeledExtract and BioSample also have Characteristics (i.e., > >> associations to OntologyEntry) now and BioSampleType association is > >> redundant. Note that in our ontology we have separated > >> LabeledExtract, > >> Biosample, and Biosource as subclasses of BiomaterialState which like > >> BiosourceProperty is a subclass of BiomaterialDescription (root). > >> > >> Chris > >> > >> On Friday, December 7, 2001, at 05:06 AM, PTSpellman@lbl.gov wrote: > >> > >>> All, > >>> > >>> Chris Stoeckert and I had a conversation yesterday about MAGE > >>> ontologies and at long last I was convinced that some > >> modifications in > >>> the biomaterial package need to be made. > >>> > >>> Specifically: > >>> BioSource:Characteristics will be much more powerful if > >> OntologyEntry > >>> can effectively become an instantiation of a class in an > >> Ontology (we > >>> all know that Objects are more powerful than hierarchies). > >> To do this > >>> OntologyEntry needs the ability to have attributes and daughter > >>> classes. I propose to solve this by allowing associations > >> to NVT and > >>> OE, this effectively allows OE's to contain the information that > >>> objects have. > >>> > >>> Also, BioMaterials at present have no way of inheiriting from > >>> BioSources that have different characteristics. One easy > >> way to solve > >>> this is to move the Characteristics from BioSource to > >> BioMaterial. A > >>> good example is if you were doing a stress test on a mice > >> and you first > >>> put it in a large cage and then put it in a small cage. Another > >>> example is if during the experiment a mutation occured that > >> change the > >>> organisms genotype. A more complex, and potentially better method > >>> would be to add characteristics to treatment so that you > >> could have an > >>> action change and or measure that alters these parameters. > >>> > >>> I have attached the BioMaterial png (unmodified) for reference. > >>> > >>> Paul > >>> > >>> > >>> > >>> Add to MAGE > >>> > >>> Attributes 0..* > >>> OntologyEntry ------------> NamedValueType > >>> > >>> Characteristics 0..* > >>> OntologyEntry -------------------> OntologyEntry > >>> > >>> Characteristics 0..* > >>> Treatment -----------------> OntologyEntry > >>> > >>> > >> > >> > >> _______________________________________________ > >> Mged-mage mailing list > >> Mged-mage@lists.sourceforge.net > >> https://lists.sourceforge.net/lists/listinfo/mged-mage > >> > > > > _______________________________________________ > > Mged-mage mailing list > > Mged-mage@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/mged-mage > > ------------------------------ Date: 13 Dec 2001 13:13:01 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] MAGE ontologies - --=-=-= Hey All, Got busy. Here is the HTML documentation of the MAGE ontologies I promised. jas. - --=-=-= Content-Type: text/html Content-Disposition: attachment; filename=ontologies.html Content-Description: MAGE Ontologies, HTML MAGE Ontology Entries
MAGE Ontology Entries
Class NameAssociation NameCardinalityDescription
ArrayGroupsubstrateType0..1Commonly, arrays will be spotted on 1x3 glass microscope slides but there is nothing that says this must be the case. This association is for scanners to inform them on the possible different formats of slides that can contain arrays.
BibliographicReferenceparameters1..NCriteria that can be used to look up the reference in a repository.
BioMaterialmaterialType1The type of material used, i.e. rna, dna, lipid, phosphoprotein, etc.
BioSampletype1The Type attribute describes the role the BioSample holds in the treatment hierarchy. This type can be an extract.
BioSequenceontologyEntries0..NOntology entries referring to common values associated with BioSequences, such as gene names, go ids, etc.
BioSequencepolymerType1A choice of protein, RNA, or DNA.
BioSequencespecies0..1The organism from which this sequence was obtained.
BioSequencetype1The type of biosequence, i.e. gene, exon, UniGene cluster, fragment, BAC, EST, etc.
BioSourcecharacteristics0..NInnate properties of the biosource, such as genotype, cultivar, tissuetype, celltype, ploidy, etc.
CompoundmerckIndex0..1The Merck Index of this Compound.
Contactroles0..N 
DatabaseEntrytype0..1The type of record (e.g. a protein in SwissProt, or a yeast strain in SGD).
DerivedBioAssaytype0..1The derivation type, for instance collapsed spot replicate, ratio, avarged intensity, bioassay replicates, etc.
Descriptionannotations0..NAllows specification of ontology entries related to the instance being described.
DesignElementcontrolType0..1If the design element represents a control, the type of control it is (normalization, deletion, negative, positive, etc.)
DesignElementGroupspecies0..1The organism from which the biosequences of this group are from.
DesignElementGrouptypes0..NThe specific type of a feature, reporter, or composite. A composite type might be a gene while a reporter type might be a cDNA clone or an oligo.
ExperimentDesigntypes0..NClassifical of an experiment. For example 'normal vs. diseased', 'treated vs. untreated', 'time course', 'tiling', etc.
ExperimentalFactorcategory0..1The category of an ExperimentalFactor could be biological (time, [glucose]) or a methodological factor (differing cDNA prepartion protocols).
FeatureDefectdefectType1Indicates the type of defect (e.g a missing feature or a moved feature).
FeatureGroupfeatureShape0..1The expected shape of the feature on the array: circular, oval, square, etc.
FeatureGrouptechnologyType0..1The technology type of this design. By specifying a technology type, higher level analysis can use appropriate algorithms to compare the results from multiple arrays. The technology type may be spotted cDNA or in situ photolithography.
FiducialfiducialType0..1A descriptive string that indicates the type of a fiducial (e.g. the chrome border on an Affymetrix array, a laser ablation mark).
Hardwaretype0..1The type of a piece of Hardware. Examples include: scanner, wash station...
Imageformat1The file format of the image typically a TIF or a JPEG.
NodeValuedataType0..1The data type of the any element.
NodeValuescale0..1The scale (linear, log10, ln, etc.) of the value.
ParameterdataType0..1The type of data generated by the parameter i.e. Boolean, float, etc...
PhysicalArrayDesignsurfaceType0..1The type of surface from a controlled vocabulary that would include terms such as non-absorptive, absorptive, etc.
Protocoltype0..1The type of a Protocol, a user should provide/use a recommended vocabulary. Examples of types include: RNA extraction, array washing, etc...
QuantitationTypedataType1The specific type for the quantitations. From a controlled vocabulary of {float, int, boolean, etc.}
QuantitationTypescale1Indication of how to interpret the value. From a suggested vocabulary of {LINEAR | LN | LOG2 |LOG10 | FOLD_CHANGE | OTHER}
ReporterfailTypes0..NIf at some time the reporter is determined to be failed this indicts the failure (doesn't report on what it was intended to report on, etc.)
ReporterwarningType0..1Similar to failType but indicates a warning rather than a failure.
Softwaretype0..1The type of a piece of Software. Examples include: feature extractor...
Treatmentaction1The event that occurred (e.g. grow, wait, add, etc...). The actions should be a reccommended vocabulary
ZoneDefectdefectType1Indicates the type of defect (e.g a missing zone or a moved zone).
- --=-=-=-- ------------------------------ Date: Fri, 14 Dec 2001 10:08:34 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Hi Jason, The current MAGE OntologyEntry is strictly referential. You can point to something (e.g. an ID in an existing ontology or controlled vocabulary) and if that something is part of a simple hierarchy (like a taxonomy or DAG) then you can infer relationships about that something easily. This is very useful and what the MGED ontology does itself when it can in OntologyEntry. The problem arises when the annotation of the sample (BioMaterial) requires more than a parts list but also requires specification of those parts (i.e. descriptors and how they fit together). For example, in the MGED Ontology, "Age" is a BiosourceProperty (which would be a MAGE BioMaterial Characteristic) that can't simply be referred to. There is no listing of all possible ages somewhere and the value of age has multiple parts (measurement and initial time point; measurement has a value and units). In MAGE all these parts would currently be combined together as text "measurement = 3, time units = days, initial time point = planting" that would need to be parsed out later. Other examples like this in the MGED Ontology are BiosourceProvider and the various classes of Treatments which are more complex than "Age." BTW. You may notice that in the MGED Ontology I have not capitalized the S in Biosource or the M in Biomaterial as has been done in MAGE. My reasoning is that I'm use capitalization to indicate where spaces would go between words. Normally I would write "biosource provider" and this (as a class not an attribute) becomes BiosourceProvider. I would not normally write "bio source provider." In case anyone was wondering. Chris On Thursday, December 13, 2001, at 03:57 PM, Jason E. Stewart wrote: > Hey All, > > I second Michael's continued request to have a submitters conference > call to go over all proposed changes to the Model (including those > 'proposals' that I've already committed to CVS ;-). > > I agree that moving Characteristics from BioSource to BioMaterial is a > good one, that was an oversight. > > I agree that there is confusion between the role of > BioMaterial:materialType, and BioSample:type. > > I'm afraid I'm not clear on the reasons why we need to make the MAGE > model of OntologyEntry more rich than it currently is, I'm not opposed > to such a plan, just that I've not been part of the discussion. > > The little I know is that Chris is creating a rich ontology for > BioSource:characteristics using an Object based ontology as opposed to > a simple list based controlled vocabulary. The MAGE OntologyEntry was > designed primarily to capture controlled vocabularies, or tree based > ontologies. > > My naive reply would be that for the description of the GE data, we > don't need to capture any more, because the detailed ontology > information (attributes and characteristics and sub-classes and > super-classes) is already captured someplace else. For example, when > annotating sequences with GO ID's, one doesn't need to store any > inheritance relationships for any given ID, because it's all stored in > the GO database. All you need to know is the ID, right? If you want to > conduct an detailed analysis of all genes that have a specific > molecular function, you will need to combine your analysis with the GO > DB. > > Likewise, in my navie thinking all we to store for an MGED > OntologyEntry is it's unique ID. My concern about the discussion that > I'm seeing is that it is proposing to build an object model for > ontologies which is beyond the scope of this work. I want to encourage > the MGED ontology to be rich, and I want to ensure that we support > it's use in MAGE, but I want to make sure that we separate the needs > for *building* an ontology from the needs of *using* that ontology. > > As I say, this is a rather naive perspective on my part, and if Chris > or Paul could help educate me as to why we need to capture something > more than: > > * What ontology the entry comes from (GO, MGED, etc) > * What the entries unique ID is > > I would be grateful. In my view, the existing attributes, 'identifier' > and 'name' (via Identifiable), 'description', 'value', and 'category' > should be sufficient level of detail for the needs of MAGE-OM. If > Chris or Paul have ideas as to how they would be used that can't be > handled using those attributes, that would simplify the discussion. > > Cheers, > jas. > > "Chris Stoeckert" writes: > >> Begin forwarded message: >> >>> From: "Miller, Michael" >>> Date: Wed Dec 12, 2001 03:42:46 PM US/Eastern >>> To: "'Chris Stoeckert'" , >>> PTSpellman@lbl.gov >> >>> Cc: mged-mage@lists.sourceforge.net, microarray-ontol@ebi.ac.uk, >>> "'LSR-GE'" >> >>> Subject: RE: [Mged-mage] Re:OntologyEntry changes >>> >>> Chris and Paul, >>> >>> I believe I understand the issue and solution here and I'm in >>> agreement. >>> >>> OntologyEntry already has an association to NVT by way of being >>> extendable, >> >>> but this proposed NVT attribute association is more specific and >>> would be >> >>> part of the formal annotation. >>> >>> I'm currently in the middle of putting together the issues people have >>> raised over the last few months. Since we are scattered across the >>> world, >> >>> we'll need some sort of process to decide what goes into v1.0, what is >>> defered to v2.0, what appeared to be an issue but isn't (because >>> people >>> agree it has to be the way it is) and issues that are good points >>> but can be >> >>> lived with. >>> >>> Once the OMG approves the standard as an official specification, they >>> provide good support for recording and voting for issues but until >>> then, for >> >>> the changes that will go in the submittal on Jan. 7th, I'm willing >>> to curate >> >>> the issues, but we need either through teleconference or email to >>> have a way >> >>> to come to consensus. (I know I'm harping on this point but as >>> editor of >> >>> the submittal I need guidance) >>> >>> This issue, by the way, I think should go into the next submittal. >>> It is >> >>> also the type of change that the OMG would think appropriate after >>> it's an >> >>> adopted specification in the finalization phase before it becomes >>> available >> >>> (hopefully from February to June) so there will be a chance to make >>> further >> >>> changes. >>> >>> thanks, >>> Michael >>> >>>> -----Original Message----- >>>> From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] >>>> Sent: Wednesday, December 12, 2001 11:32 AM >>>> To: PTSpellman@lbl.gov >>>> Cc: mged-mage@lists.sourceforge.net; microarray-ontol@ebi.ac.uk >>>> Subject: [Mged-mage] Re: >>>> >>>> >>>> Hi Paul, >>>> I think your proposal to associate NameValueType and OntologyEntry to >>>> OntologyEntry should work nicely. >>>> Note that what MAGE calls Characteristics (an >>>> association/attribute of >>>> BioSource) is what our ontology calls BiosourceProperty (a >>>> class which >>>> is a subclass of BiomaterialDescription). >>>> Promoting Characteristics to Biomaterials should work. This >>>> means that >>>> LabeledExtract and BioSample also have Characteristics (i.e., >>>> associations to OntologyEntry) now and BioSampleType association is >>>> redundant. Note that in our ontology we have separated >>>> LabeledExtract, >>>> Biosample, and Biosource as subclasses of BiomaterialState which like >>>> BiosourceProperty is a subclass of BiomaterialDescription (root). >>>> >>>> Chris >>>> >>>> On Friday, December 7, 2001, at 05:06 AM, PTSpellman@lbl.gov wrote: >>>> >>>>> All, >>>>> >>>>> Chris Stoeckert and I had a conversation yesterday about MAGE >>>>> ontologies and at long last I was convinced that some >>>> modifications in >>>>> the biomaterial package need to be made. >>>>> >>>>> Specifically: >>>>> BioSource:Characteristics will be much more powerful if >>>> OntologyEntry >>>>> can effectively become an instantiation of a class in an >>>> Ontology (we >>>>> all know that Objects are more powerful than hierarchies). >>>> To do this >>>>> OntologyEntry needs the ability to have attributes and daughter >>>>> classes. I propose to solve this by allowing associations >>>> to NVT and >>>>> OE, this effectively allows OE's to contain the information that >>>>> objects have. >>>>> >>>>> Also, BioMaterials at present have no way of inheiriting from >>>>> BioSources that have different characteristics. One easy >>>> way to solve >>>>> this is to move the Characteristics from BioSource to >>>> BioMaterial. A >>>>> good example is if you were doing a stress test on a mice >>>> and you first >>>>> put it in a large cage and then put it in a small cage. Another >>>>> example is if during the experiment a mutation occured that >>>> change the >>>>> organisms genotype. A more complex, and potentially better method >>>>> would be to add characteristics to treatment so that you >>>> could have an >>>>> action change and or measure that alters these parameters. >>>>> >>>>> I have attached the BioMaterial png (unmodified) for reference. >>>>> >>>>> Paul >>>>> >>>>> >>>>> >>>>> Add to MAGE >>>>> >>>>> Attributes 0..* >>>>> OntologyEntry ------------> NamedValueType >>>>> >>>>> Characteristics 0..* >>>>> OntologyEntry -------------------> OntologyEntry >>>>> >>>>> Characteristics 0..* >>>>> Treatment -----------------> OntologyEntry >>>>> >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Mged-mage mailing list >>>> Mged-mage@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>>> >>> >>> _______________________________________________ >>> Mged-mage mailing list >>> Mged-mage@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/mged-mage >>> > > _______________________________________________ > Mged-mage mailing list > Mged-mage@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mged-mage > ------------------------------ Date: 17 Dec 2001 08:15:44 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Hey Chris, "Chris Stoeckert" writes: > For example, in the MGED Ontology, "Age" is a BiosourceProperty > (which would be a MAGE BioMaterial Characteristic) that can't simply > be referred to. There is no listing of all possible ages somewhere > and the value of age has multiple parts (measurement and initial > time point; measurement has a value and units). In MAGE all these > parts would currently be combined together as text "measurement = 3, > time units = days, initial time point = planting" that would need to > be parsed out later. Other examples like this in the MGED Ontology > are BiosourceProvider and the various classes of Treatments which > are more complex than "Age." Ah. Ok, this is more clear, thanks. It makes me a bit nervous, though. I'm a bit afraid the following is going to sound like a criticism of the ontology work, and I don't mean it that way. I believe that it is a shortcoming of the MAGE work. In order to make the MGED ontology rich enough to be useful, it will create it's own object hierarchy, none of which is encoded in the MAGE model (in fact no one has to use the MGED ontology, they could use their own if they choose). So in order to write a query that uses the age property of a BioSource, I'll have to know write something that is very specific to the internal representation of the MAGE ontology: find all BioSource which have an 'age' OntologyEntry whose characteristics list has an 'initial time point' entry whose value is 'after planting' AND whose characteristics list has an 'units' entry whose value is 'days' AND whose value is '7' There's two issues that bother me about this: 1) it's very MGED ontology dependent, and is not part of the MAGE model. 2) This entry has two roles: a measurement and an OntologyEntry If our goal is to eventually make the MGED Ontology part of the MAGE model, then 1) is not an issue. 2) is a bigger problem, I think. We had hoped that all the characteristics of BioSource were OntologyEntries, but I don't think that they are, I think that some are Measurements Some are clearly OntologyEntries: * taxon * phenotype * genotype * strain But as Chris has pointed out, age is different, it is a value and a unit, which is the MAGE model of a Measurement: * 7 days after planting This is a relative time Measurement: Value: 7 Unit: days Relative to: date of planting Interval: after I believe that the different pieces of this are OntologyEntries except for the value (7). MAGE doesn't have a relative time Measurement though, oops. I wonder if there are other examples like this. Once I get back to ABQ (today), I'll take a look. Chris, how do you feel about this? Should this be represented as a Measurement or an OntologyEntry? Should BioSource have a list of Measurements as well as a list of OntologyEntries? Others? jas. ------------------------------ End of microarray-ontol-digest V1 #16 *************************************