microarray-ontol-digest Monday, December 31 2001 Volume 01 : Number 017 ---------------------------------------------------------------------- Date: Tue, 18 Dec 2001 10:19:05 -0800 From: "Paul Spellman" Subject: RE: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Jason, try looking at the age slightly differently. OE has category value source, it could be coded as category age:initial time point:after planting:days value 7 source MGED paul - -----Original Message----- From: owner-microarray-ontol@ebi.ac.uk [mailto:owner-microarray-ontol@ebi.ac.uk]On Behalf Of Jason E. Stewart Sent: Monday, December 17, 2001 7:16 AM To: microarray-ontol@ebi.ac.uk; mged-mage@lists.sourceforge.net 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. ------------------------------ Date: 18 Dec 2001 13:09:34 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes "Paul Spellman" writes: > try looking at the age slightly differently. OE has category value > source, it could be coded as > > category age:initial time point:after planting:days > value 7 > source MGED In all other cases the value will be used to encode the entry: category BioAssay:type value derived_other source MGED category Image:format value JPEG source MGED category BioSource:taxon value E. coli source MGED the one for age doesn't make sense. That's because age is a measurement. The unit of the measurement is an ontology entry, but the value isn't. jas. ------------------------------ Date: Tue, 18 Dec 2001 13:25:02 -0800 From: "Paul Spellman" Subject: RE: [microarray-ontol] Fwd: [Mged-mage] Re:OntologyEntry changes Do we have a date for this yet? tomorrow morning works for me, as does thurs afternoon, or friday morn. paul - -----Original Message----- From: owner-microarray-ontol@ebi.ac.uk [mailto:owner-microarray-ontol@ebi.ac.uk]On Behalf Of Jason E. Stewart Sent: Thursday, December 13, 2001 12:58 PM To: microarray-ontol@ebi.ac.uk; mged-mage@lists.sourceforge.net 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: Wed, 19 Dec 2001 13:27:15 +0000 From: Helen Parkinson Subject: [microarray-ontol] GeneticVariation Hi Chris, I have been looking at this and think the definition is a bit counter intuitive: GeneticVariation - ---------------- documentation: The genetic modification introduced into the organism from which the biomaterial was derived. Examples of genetic variation include specification of a transgene or the gene knocked-out. genetic variation suggests to me natural genetic variation which is covered by IndividualGeneticCharacteristic, what about renaming it to GeneticModification cheers Helen ------------------------------ Date: Wed, 19 Dec 2001 13:33:09 +0000 From: Helen Parkinson Subject: [microarray-ontol] [Fwd: questions about sex - bacteria, parasites and yeasts] hi guys, we could use some help on the definition of sex and its instances in the ontology, it came in for some criticism at a recent meeting at the EBI. If you know of an expert in any of these areas please forward to them, it has already gone to local people here in Cambridge but the more input the better, thanks Helen sex definition: The gender of the organism or the reproductive organs present on the organism (prior to any modification) that the biomaterial is derived from instances both_sexes male female unknown_sex this was designed to cover cases where there is an actual fertilization event How should sex be described where there is a transfer of genetic material but not a fertilization: fungi - ----- do pombe and cerevisiae exchange genetic material? are there sexes or mating types, can they be described by strain names or terms? If so what would be a good definition of a mating type anyone know anything about other fungi, candida or neurospora? or know anyone who does parasites - --------- is there exchange of genetic material, are the terms that cover it unique to species, can it be covered by descriptions of the strains, is there a list of the strains anywhere? or even better a cv and how would mating type be defined bugs (big plasmids in the vernacular) - ---- do gram +ve and -ve both exchange material? is it always as plasmids, do plasmids come under the general definition of genotype or strain? is there a distinction between them should it be called mating type? and how would that be defined? we also have classes IndividualGeneticCharacterstics - -------------------------------- The genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes. Strain - ------ Animals or plants that have a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings these could be used to cover some information about mating type, would this be appropriate. the definition of sex has been purposely defined not to be a chromosomal definition ------------------------------ Date: 19 Dec 2001 07:58:43 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] [Fwd: questions about sex - bacteria, parasites and yeasts] "Helen Parkinson" writes: > sex > > definition: > > The gender of the organism or the reproductive organs > present on the organism (prior to any modification) that the > biomaterial is derived from > > instances > > both_sexes > male > female > unknown_sex > > this was designed to cover cases where there is an actual > fertilization event > > How should sex be described where there is a transfer of > genetic material but not a fertilization: Hey Helen, Not being an expert, I'll stay out of this, but my feeling is that we should use the species-specific terminology that the biologists are familiar with - which may mean some sort of subclassing based on taxon id. jas. ------------------------------ Date: Wed, 19 Dec 2001 15:11:45 +0000 From: Helen Parkinson Subject: Re: [microarray-ontol] [Fwd: questions about sex - bacteria, parasites and yeasts] Hi, after a chat with Midori (GO editor) I have managed to simplify this a bit. I don't really want to go the species specific route. The problem is that if we go species specific then we need really to point at external ontologies, and in many cases there are no external ontologies, so something analagous to go is more useful at least in the short term. Of course people can still provide species specific instances if they like but they still have to go somewhere in the ontology and we could easily just make a mess. Hence the effort to canvas some expert opinion. There are some interesting recent mails in the go database about sex as a process, (but without pictures) http://www.geneontology.org/go_email.html I think a structure like this might work: %sex %gender male -producing small numerous gametes female -producing small numbers of large gametes both unknown %mating type instances eg alpha for yeast I am working on some definitions of sex, gender and mating type, these are not hard and fast terms, just thoughts, cheers helen "Jason E. Stewart" wrote: > > "Helen Parkinson" writes: > > > sex > > > > definition: > > > > The gender of the organism or the reproductive organs > > present on the organism (prior to any modification) that the > > biomaterial is derived from > > > > instances > > > > both_sexes > > male > > female > > unknown_sex > > > > this was designed to cover cases where there is an actual > > fertilization event > > > > How should sex be described where there is a transfer of > > genetic material but not a fertilization: > > Hey Helen, > > Not being an expert, I'll stay out of this, but my feeling is that we > should use the species-specific terminology that the biologists are > familiar with - which may mean some sort of subclassing based on taxon > id. > > jas. ------------------------------ Date: Wed, 19 Dec 2001 16:46:20 +0000 From: Helen Parkinson Subject: [microarray-ontol] Re: sex gender mating type Hi, suggested revision of sex, now has two subclasses and new definitions and a few instances, comments or more instances anyone or a better word than gender? cheers helen > -------------- > &sex > &gender > &mating type > -------------- > > %sex > > term applied to any organism able to undergo sexual > reproduction in order to differentiate the two individuals > or types involved. Sexual reproduction is defined as the > ability to exchange genetic material with the potential of > recombinant progeny. > > %gender subclass of sex applicable to heterogametic species (i.e. those in which the sexes produce gametes of markedly different size) > > instances > --------- > male -producing small numerous gametes > female -producing small numbers of large gametes > both -suggest replacing with: mosaic and hermaphrodite > mixed -a population of individuals with any or all of the above present > unknown > %mating type > instances divided up into species for ease of use, probably incomplete, possibly wrong > --------- > Candida albicans > H > H+ > > Saccharomyces cerevisiae > a > alpha > a/alpha > Neurospora Crassa > A > a > > Schizosaccharomyces pombe > h+ > h- - ---------------------------------------------------------------------------------- thanks to Midori and Sanger people for help with the definitions and instances etc ------------------------------ Date: Wed, 19 Dec 2001 09:38:13 -0800 (PST) From: Mike Cherry Subject: Re: [microarray-ontol] Re: sex gender mating type Very minor comment, to be completely general you might say "the different individuals or types involved". I believe Tetrahymena has seven mating types. Althought I understand that only two conjugate at a time. There are always exceptions to the rules in biology. - -Mike > > > > term applied to any organism able to undergo sexual > > reproduction in order to differentiate the two individuals > > or types involved. Sexual reproduction is defined as the > > ability to exchange genetic material with the potential of > > recombinant progeny. > > > > %gender > subclass of sex applicable to heterogametic species (i.e. > those in which > the sexes produce gametes of markedly different size) > > > > instances > > --------- > > male -producing small numerous gametes > > female -producing small numbers of large gametes > > both -suggest replacing with: mosaic and hermaphrodite > > mixed -a population of individuals with any or all of the above present > > unknown > > %mating type > > instances divided up into species for ease of use, probably incomplete, possibly wrong > > --------- > > Candida albicans > > H > > H+ > > > > Saccharomyces cerevisiae > > a > > alpha > > a/alpha > > > Neurospora Crassa > > A > > a > > > > Schizosaccharomyces pombe > > h+ > > h- > > ---------------------------------------------------------------------------------- > thanks to Midori and Sanger people for help with the > definitions and instances etc > - -- J. Michael Cherry, Ph.D. Internet: cherry@stanford.edu Associate Professor (Research) Department of Genetics Medical Center, Room M341 Stanford University School of Medicine Voice: 650-723-7541 Stanford, California 94305-5120 FAX: 650-723-7016 http://genome-www.stanford.edu/~cherry Cellular: 650-868-1848 ------------------------------ Date: Thu, 20 Dec 2001 14:14:59 +0000 From: Susanna Sansone Subject: Re: [microarray-ontol] Re: sex gender mating type >>bugs (big plasmids in the vernacular) >>---- >>do gram +ve and -ve both exchange material? >>is it always as plasmids, do plasmids come under the general >>definition of genotype or strain? >>is there a distinction between them >>should it be called mating type? >>and how would that be defined? Some gram +ve and -ve bacteria exchange genetic material (with a different mechanism though) Three cell types (mating type or cross type): F+, donor, "male" (F-factor as autonomous plasmid) Hfr, donor, "male" (F-factor integrated into in the chromosome) F-, recipient, "female" So could be: %mating type instances: F+ Hfr F- Susanna Helen Parkinson wrote: > > Hi, > > suggested revision of sex, now has two subclasses and new > definitions and a few instances, > > comments or more instances anyone or a better word than > gender? > > cheers > > helen > > > -------------- > > &sex > > &gender > > &mating type > > -------------- > > > > %sex > > > > term applied to any organism able to undergo sexual > > reproduction in order to differentiate the two individuals > > or types involved. Sexual reproduction is defined as the > > ability to exchange genetic material with the potential of > > recombinant progeny. > > > > %gender > subclass of sex applicable to heterogametic species (i.e. > those in which > the sexes produce gametes of markedly different size) > > > > instances > > --------- > > male -producing small numerous gametes > > female -producing small numbers of large gametes > > both -suggest replacing with: mosaic and hermaphrodite > > mixed -a population of individuals with any or all of the above present > > unknown > > %mating type > > instances divided up into species for ease of use, probably incomplete, possibly wrong > > --------- > > Candida albicans > > H > > H+ > > > > Saccharomyces cerevisiae > > a > > alpha > > a/alpha > > > Neurospora Crassa > > A > > a > > > > Schizosaccharomyces pombe > > h+ > > h- > > ---------------------------------------------------------------------------------- > thanks to Midori and Sanger people for help with the > definitions and instances etc - -- ******************************* Susanna Assunta Sansone, PhD Microarray Informatics EBI - The European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus Cambridge CB10 1SD, UK email: sansone@ebi.ac.uk direct: +44 (0)1223 494 691 fax: +44 (0)1223 494 468 http://www.ebi.ac.uk/microarray ******************************* ------------------------------ Date: 20 Dec 2001 09:47:09 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Re: sex gender mating type Hey All, I remember that GeneX had a controlled vocabulary for Sex/MatingType already, so I dug it up. Turns out most of what we had has already been discussed, but I'm including in case something is useful. Appologies for the XML challenged. jas. - -- to this organism"/> ------------------------------ Date: Sat, 22 Dec 2001 12:15:58 +0000 (GMT) From: Alvis Brazma Subject: [microarray-ontol] MGED 4 MGED 4 Registration Enhancements February 13-16, 2002 Hynes Convention Center Sheraton Boston Marriott Copley Place The MGED 4 Meeting Site (php.aaas.org/mged) has several enhancement to aid your planning for this meeting. Links to hotel and airlines have been added. A pdf version of the registration form will be posted shortly, should you be experiencing difficulty with web registration. We have fixed several problems that were occurring with the online registration process (but there are, no doubt, many more we could encounter!).   If you have registration difficulties you may contact the registrar at mrosenth@aaas.org or Michael Strauss, AAAS Meeting Director, at mstrauss@aaas.org REMEMBER: Registration deadline is January 21. After that date the fee for registration will go from $260 to $315. ------------------------------ Date: Thu, 27 Dec 2001 15:48:25 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] GeneticVariation Hi Helen, Happy Holidays everyone! I'm not wild about the names either but you can blame Alvis and the annotation group for these. There already exists a GeneticModification which is a subclass of Treatment (through Modification). GeneticVariation may describe the same thing but as a pre-existing state. How about this? Delete GeneticVariation from BiosourceOntologyEntry Make GeneticModification a subclass of BiosourceProperty and of Modification (and by extension Treatment). Will have to see if the Fact Reasoner accepts this as well. Chris On Wednesday, December 19, 2001, at 08:27 AM, Helen Parkinson wrote: > Hi Chris, > > I have been looking at this and think the definition is a > bit counter intuitive: > > > GeneticVariation > ---------------- > > documentation: > The genetic modification introduced into the organism > from which the biomaterial was derived. Examples of genetic > variation include specification of a transgene or the gene > knocked-out. > > > genetic variation suggests to me natural genetic variation > which is covered by IndividualGeneticCharacteristic, > > what about renaming it to > > GeneticModification > > cheers > > Helen > ------------------------------ Date: Thu, 27 Dec 2001 16:23:06 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] Re: sex gender mating type Thanks everyone (especially Helen) for the recent discussion on the biomaterial description of sex. In trying to come up with a consensus to incorporate into the ontology, I am stuck when trying to provide instances of mating type as these are species specific. The type "a" is used by S. cerevisiae and N. crassa. Are they the same? Are H and h different? Is it F+ or f+? Do we need to go the "sensu" route (i.e. in the sense of) as the GO people have? I would rather not because the constraints are then placed in the text. We could add a subclass to "MatingType" for bacteria called "ConjugationType" to help clarify what term to use. From: BioTech Life Science Dictionary: http://biotech.icmb.utexas.edu/search/dict-search.phtml > bacterial conjugation > Definition: > The process of transferring a certain plasmid of DNA known as the F > plasmid (or sex plasmid) from bacteria individuals who have it (known > as "males") to bacteria individuals who do not already have it (known > as "females") by way of direct contact between the bacteria individuals > called a conjugation bridge. Once transfer is completed, the female > individual becomes a male individual and both parties have a copy of > the F plasmid. They didn't have a definition for mating type or gender but did give a search field for the On-line medical dictionary. http://www.graylab.ac.uk/cgi-bin/omd?action=Home&query= Note: "Gender is a grammatical distinction and applies to words only. Sex is natural distinction and applies to living objects." (R. Morris) Is the "Sex" class the natural place for mating type information or would that be included as "IndividualGeneticCharacteristic" or "Strain" as Helen indicated in the beginning of the discussion. The "Sex" class could be constrained to organisms producing gametes if one normally lists mating type along with allele or strain info. Cheers, Chris On Wednesday, December 19, 2001, at 11:46 AM, Helen Parkinson wrote: > Hi, > > suggested revision of sex, now has two subclasses and new > definitions and a few instances, > > > comments or more instances anyone or a better word than > gender? > > cheers > > helen > > >> -------------- >> &sex >> &gender >> &mating type >> -------------- >> >> %sex >> >> term applied to any organism able to undergo sexual >> reproduction in order to differentiate the two individuals >> or types involved. Sexual reproduction is defined as the >> ability to exchange genetic material with the potential of >> recombinant progeny. >> >> %gender > subclass of sex applicable to heterogametic species (i.e. > those in which > the sexes produce gametes of markedly different size) >> >> instances >> --------- >> male -producing small numerous gametes >> female -producing small numbers of large gametes >> both -suggest replacing with: mosaic and hermaphrodite >> mixed -a population of individuals with any or all of the above >> present >> unknown >> %mating type >> instances divided up into species for ease of use, probably >> incomplete, possibly wrong >> --------- >> Candida albicans >> H >> H+ >> >> Saccharomyces cerevisiae >> a >> alpha >> a/alpha >> > Neurospora Crassa >> A >> a >> >> Schizosaccharomyces pombe >> h+ >> h- > > ---------------------------------------------------------------------------------- > thanks to Midori and Sanger people for help with the > definitions and instances etc > ------------------------------ Date: 27 Dec 2001 22:53:12 -0700 From: jason@openinformatics.com (Jason E. Stewart) Subject: Re: [microarray-ontol] Re: sex gender mating type Hey Chris, I'm sending the reply to the list as I figure this is a generally useful discussion. "Chris Stoeckert" writes: > >> I'm hoping to use the holidays to give me space to actually think > >> about these issues. Angel filled me in on the discussion you had > >> today. There are multiple examples beside age where a > >> self-referential ontology entry would be needed and I hope to > >> provide these to you next week. I'll put my comments after your examples. > Some other cases like age: > BiosourceProvider has 3 attributes. One "biosource_type" is an > enumerated list. The others are has_owner(Person) and > has_donor(Organization). Person is a class with attributes: > first_name, last_name, mid_initials, and > has_organization(Organization). Organization has a name. Both > Person and Organization are subclasses of Contact which has > address, email, fax, toll_free_phone, phone, and has_URI(URI). > > EnvironmentalHistory is a class with subclasses such as > CultureCondition which in turn has subclasses such as > Nutrients. CultureCondition has the attribute > has_measurement(Measurement) and Nutrients has the attribute > nutrient_component(Compound). Compound is a subclass of > OntologyEntry. > > Treatment is a class with subclasses such as > Modification. Modification has a subclass SomaticModification > which in turn has the attribute > has_part_modified(OrganismPart) where OrganismPart is an > OntologyEntry. Note that Treatment has_protocol(Protocol) and > Modification has a modification_type. > > There are other examples but you get a sense for the complexity of > these terms that a name, value, source can't cover alone. Also, you > see the need to refer to other ontologies (e.g., compound) and objects > used by MAGE (e.g., Contact, Protocol). Having read the three examples that you presented it is clear to me that before we go much further we should move up a level in our discussion. I really think we need to discuss where the boundaries of the ontology and the MAGE model lie - where they overlap, and why. I believe that along with MIAME, the ontology and MAGE will be important contributions of MGED to the community, and I believe they should all coexist happily. It feels to me that we developed MAGE without paying too much attention (until just recently) to what was going on with the ontology project. I'm getting involved not because I want to prove how clever my ideas are, but because I want to see the ontology become something that's really useful for people. Two years ago I knew nothing about XML. One year ago I knew nothing about UML. Two months ago I knew nothing about ontologies. So at best, I'm an opinionated novice. I'm tossing in all these caveats because I think that there's been a lot of work put into this already, and I want to be careful about stepping on other people toes. But I think that unless we talk about these issues we're likely to start bumping our heads into one another. Let me set some ground rules that I think will help: * I think we should be willing to change MIAME, MAGE, or the ontology in order to make them work together in a synergistic manner. * I'm *not* convinced that MAGE is *the* correct way of modelling anything, and so if things are better done within the ontology and I can make MAGE smaller, I am *thrilled* to do so. * I believe that we should let ourselves be guided by 'use cases' - or ways that we anticipate these three pieces will be used by the community. If we have an important use case that we cannot support by the current model, we should change things. Likewise we shouldn't add new 'features' unless we can identify a use case that needs that feature. This just provides a common ground for everyone to understand what the motivations for our decisions are. I believe that MAGE would be much more understandable if we would document more of the use cases that we have explored over time. First, what does MAGE do? Three things: ======================================= 1) Describes an *object model* that enables us to build API's in Perl, Java, etc that tell us how to build computer data structures to hold the data 2) Describes a communication format MAGE-ML that enables us to encode the data in a text file that can be transfered over the internet. 3) Hopefully it will soon describe a relation DB mapping Second, how will MAGE get used? A couple of ways: ================================================= * Software to read MAGE-ML - converts it into programming language objects that store the data temporarily * Software that reads MIAME data from a database - likewise temporary storage of data into objects * Software that writes data to a MAGE database - like the MIAMExpress software * Software to write MAGE-ML - convert data into MAGE objects and the existing MAGE-ML writers can do the rest * Software to analyze microarray data - since it will likely want to read from and store to a MAGE DB Those are MAGE's high-level use cases. What does the ontology do? ========================== An ontology is a description of knowledge. It's a very broad thing, and it can become anything that you want to make of it. I'm not sure what you (or others) feel about this. At the very least I see it providing three things: 1) A list of properties that samples can have (taxon, cultivar, strain, organ type, tissue type, cell type, etc) 2) A list of values that each of those properties can have (for organ type: brain, heart, liver, etc) 3) Definitions for all of the properties and the values. I believe that this is the fundamental value of the ontology: by providing a concrete terminology we can assign meaning to our data that is unambiguous. And we can use those unambiguous meanings to determine whether two pieces of data (two samples) are similar or dis-similar. How will it be used? ==================== >From reading the ontology group home page, it seems that the primary mission of the group is develop the sample ontology as a way for researchers to annotate the samples used in their experiments. That helps MIAME, and it fits nicely with MAGE. Likewise I'm not sure what you (or others) feel about this. At least, I see two things: 1) In data transmitted by MAGE-ML, a researcher uses ontology terms to describe the samples used in the experiment 2) When making queries to a DB, a researcher uses ontology terms to find experiments of relevance Once again, there can be more, but these are the minimal ones: assigning terms to data, retrieving similar data and not dis-similar ones. How are MAGE and the Ontology similar? ====================================== At a high level, an object model and an ontology are the same thing: descriptions of knowledge and the relationships and properties of the information. An object model just describes it in a way that enables us to build programming language objects from the information. What I'd like to propose is: 1) that we let the object model (MAGE) handle the information that is variable and chaning 2) that we let the ontology handle the information that is invariant and unchanging. For example, 'Measurement' is an object with two components: a value and a unit. The value is a variable and therefore Measurement as an object is in the realm of MAGE, while unit which is invariant (meaning we can define all the units that we need - Chemistry Markup Language did it for us) and should belong to the ontology. Maybe this is an overly bold suggestion, but I understand how to use it within the MAGE-MIAME framework. Like GO it enables us to build an unambiguous system of information to describe our experiments from the side of the variable data: MAGE, and the invariant data: the ontology. Because the ontolgy data is invariant each concept can have a unique identifier in a central database, and an MAGE object that wants to reference an ontology entry can just use that ontology entry's identifier: e.g. MGED:100456. Right now, that is all that the MAGE OntologyEntry object provides: the ability to reference a database entry in some other DB, as well as a bit of extra information such as name and category so that it can be useful without performing the lookup. jas. ------------------------------ Date: Mon, 31 Dec 2001 12:49:51 -0500 From: Chris Stoeckert Subject: Re: [microarray-ontol] Re: sex gender mating type Hey Jason, I'm delighted that you MAGE guys are joining our discussions! You are right that this is a fundamental issue and one that should be driven by "use cases." The issue that I'm referring to is the extent and purpose of the MGED ontology. Should it simply be a collection of pointers to controlled vocabulary terms or IDs as you proposed in your mail? My answer is "No." This was the initial goal and the purpose of the Ontology Resources at the MGED OWG home page (http://www.cbil.upenn.edu/Ontology/index.html#ontology.resources). This does address the use case of "assigning terms to data, retrieving similar data and not dis-similar ones" but not completely as I'll discuss later. Ontologies can be more than (hierarchical) controlled vocabulary terms with definitions. They can describe objects (subclassing AND foreign keys). They can provide constraints as to how those objects can be built so that a computer can use an ontology to reason whether an object makes sense (semantic checking) and infer parts of the object that haven't been explicitly added. There are two very pressing use cases that require this reasoning capability. The first is "Is this a MIAME-compliant document?" Because many fields describing the sample/biomaterial in a microarray experiment are context dependent, checking for null values is not very useful. An ontology could be used to determine if the fields (and their values) are complete and make logical sense. The second use case is minimizing effort to enter annotation. Rather than go through page after page of forms that are designed for general input, an ontology could be used to determine what are appropriate fields given some initial input and fill some of the remaining fields in. The current MGED ontology does not yet have this expressive power but can with addition of constraints. Getting back to the use case of "retrieving similar data and not dis-similar ones," the resolution of what is similar will be determined by the expressive power of the ontology. In the simplest case, a list of properties, their values and sources can be compared. While valuable (even if you just get the same species), this approach is limited to properties that can be described by a single value. Complex properties (objects with attributes) such as age, biosource provider, environmental history (e.g.,culture condition), and treatment (e.g.,somatic modification) can not be each captured with a single controlled vocabulary term or external ID. Like MAGE, the MGED ontology will be best understood when software is written to make use of it. Right now we need to flesh out the MGED ontology a bit more but I believe that Helen Parkinson, Susanna Sansone, and others in Alvis Brazma's group are designing their annotation forms for ArrayExpress using this. We will be revising our forms for RAD and building this into our MAGE exporter for RAD. I would love to hear what others are doing. Chris On Friday, December 28, 2001, at 12:53 AM, Jason E. Stewart wrote: > Hey Chris, > > I'm sending the reply to the list as I figure this is a generally > useful discussion. > > "Chris Stoeckert" writes: > >>>> I'm hoping to use the holidays to give me space to actually think >>>> about these issues. Angel filled me in on the discussion you had >>>> today. There are multiple examples beside age where a >>>> self-referential ontology entry would be needed and I hope to >>>> provide these to you next week. > > I'll put my comments after your examples. > >> Some other cases like age: >> BiosourceProvider has 3 attributes. One "biosource_type" is an >> enumerated list. The others are has_owner(Person) and >> has_donor(Organization). Person is a class with attributes: >> first_name, last_name, mid_initials, and >> has_organization(Organization). Organization has a name. Both >> Person and Organization are subclasses of Contact which has >> address, email, fax, toll_free_phone, phone, and has_URI(URI). >> >> EnvironmentalHistory is a class with subclasses such as >> CultureCondition which in turn has subclasses such as >> Nutrients. CultureCondition has the attribute >> has_measurement(Measurement) and Nutrients has the attribute >> nutrient_component(Compound). Compound is a subclass of >> OntologyEntry. >> >> Treatment is a class with subclasses such as >> Modification. Modification has a subclass SomaticModification >> which in turn has the attribute >> has_part_modified(OrganismPart) where OrganismPart is an >> OntologyEntry. Note that Treatment has_protocol(Protocol) and >> Modification has a modification_type. >> >> There are other examples but you get a sense for the complexity of >> these terms that a name, value, source can't cover alone. Also, you >> see the need to refer to other ontologies (e.g., compound) and objects >> used by MAGE (e.g., Contact, Protocol). > > Having read the three examples that you presented it is clear to me > that before we go much further we should move up a level in our > discussion. I really think we need to discuss where the boundaries of > the ontology and the MAGE model lie - where they overlap, and why. I > believe that along with MIAME, the ontology and MAGE will be important > contributions of MGED to the community, and I believe they should all > coexist happily. It feels to me that we developed MAGE without paying > too much attention (until just recently) to what was going on with the > ontology project. > > I'm getting involved not because I want to prove how clever > my ideas are, but because I want to see the ontology become something > that's really useful for people. Two years ago I knew nothing about > XML. One year ago I knew nothing about UML. Two months ago I knew > nothing about ontologies. So at best, I'm an opinionated novice. > > I'm tossing in all these caveats because I think that there's been a > lot of work put into this already, and I want to be careful about > stepping on other people toes. But I think that unless we talk about > these issues we're likely to start bumping our heads into one another. > > > Let me set some ground rules that I think will help: > > * I think we should be willing to change MIAME, MAGE, or the ontology > in order to make them work together in a synergistic manner. > > * I'm *not* convinced that MAGE is *the* correct way of modelling > anything, and so if things are better done within the ontology and I > can make MAGE smaller, I am *thrilled* to do so. > > * I believe that we should let ourselves be guided by 'use cases' - or > ways that we anticipate these three pieces will be used by the > community. If we have an important use case that we cannot support > by the current model, we should change things. Likewise we shouldn't > add new 'features' unless we can identify a use case that needs that > feature. This just provides a common ground for everyone to > understand what the motivations for our decisions are. I believe > that MAGE would be much more understandable if we would document > more of the use cases that we have explored over time. > > First, what does MAGE do? Three things: > ======================================= > > 1) Describes an *object model* that enables us to build API's in Perl, > Java, etc that tell us how to build computer data structures to > hold the data > > 2) Describes a communication format MAGE-ML that enables us to encode > the data in a text file that can be transfered over the internet. > > 3) Hopefully it will soon describe a relation DB mapping > > Second, how will MAGE get used? A couple of ways: > ================================================= > > * Software to read MAGE-ML - converts it into programming language > objects that store the data temporarily > > * Software that reads MIAME data from a database - likewise temporary > storage of data into objects > > * Software that writes data to a MAGE database - like the MIAMExpress > software > > * Software to write MAGE-ML - convert data into MAGE objects and the > existing MAGE-ML writers can do the rest > > * Software to analyze microarray data - since it will likely want to > read from and store to a MAGE DB > > Those are MAGE's high-level use cases. > > What does the ontology do? > ========================== > > An ontology is a description of knowledge. It's a very broad thing, > and it can become anything that you want to make of it. I'm not sure > what you (or others) feel about this. At the very least I see it > providing three things: > > 1) A list of properties that samples can have (taxon, cultivar, > strain, organ type, tissue type, cell type, etc) > > 2) A list of values that each of those properties can have (for organ > type: brain, heart, liver, etc) > > 3) Definitions for all of the properties and the values. > > I believe that this is the fundamental value of the ontology: by > providing a concrete terminology we can assign meaning to our data > that is unambiguous. And we can use those unambiguous meanings to > determine whether two pieces of data (two samples) are similar or > dis-similar. > > How will it be used? > ==================== > >> From reading the ontology group home page, it seems that the primary > mission of the group is develop the sample ontology as a way for > researchers to annotate the samples used in their experiments. That > helps MIAME, and it fits nicely with MAGE. Likewise I'm not sure what > you (or others) feel about this. > > At least, I see two things: > > 1) In data transmitted by MAGE-ML, a researcher uses ontology terms to > describe the samples used in the experiment > > 2) When making queries to a DB, a researcher uses ontology terms to > find experiments of relevance > > Once again, there can be more, but these are the minimal ones: > assigning terms to data, retrieving similar data and not dis-similar > ones. > > How are MAGE and the Ontology similar? > ====================================== > > At a high level, an object model and an ontology are the same thing: > descriptions of knowledge and the relationships and properties of the > information. An object model just describes it in a way that enables > us to build programming language objects from the information. > > What I'd like to propose is: > > 1) that we let the object model (MAGE) handle the information that is > variable and chaning > > 2) that we let the ontology handle the information that is invariant > and unchanging. > > For example, 'Measurement' is an object with two components: a value > and a unit. The value is a variable and therefore Measurement as an > object is in the realm of MAGE, while unit which is invariant (meaning > we can define all the units that we need - Chemistry Markup Language > did it for us) and should belong to the ontology. > > Maybe this is an overly bold suggestion, but I understand how to use > it within the MAGE-MIAME framework. Like GO it enables us to build an > unambiguous system of information to describe our experiments from the > side of the variable data: MAGE, and the invariant data: the > ontology. Because the ontolgy data is invariant each concept can have > a unique identifier in a central database, and an MAGE object that > wants to reference an ontology entry can just use that ontology > entry's identifier: e.g. MGED:100456. > > Right now, that is all that the MAGE OntologyEntry object provides: > the ability to reference a database entry in some other DB, as well as > a bit of extra information such as name and category so that it can be > useful without performing the lookup. > > jas. > ------------------------------ End of microarray-ontol-digest V1 #17 *************************************