microarray-ontol-digest Wednesday, September 5 2001 Volume 01 : Number 011 ---------------------------------------------------------------------- Date: Sat, 25 Aug 2001 19:03:10 -0400 From: Chris Stoeckert Subject: [microarray-ontol] biomaterial description ontology (second try) Hmm, tried to send this put got a message too long error. Will not attach the rdfs file - mail me if you want it otherwise it'll be posted. Chris Dear group, I've made some progress putting the concepts listed on the "Building ontologies" page into RDF schema using the OIL editor. I will post these on the site probably on Monday. Meanwhile here is a hand-crafted hierarchy to give you a flavor for what I've done. The indentation indicates inheritance (i.e., BiomaterialState is a subclass of BiomaterialDescription and has the attribute "has_been_manipulated_by"). Next steps are to 1) provide as many instances as I can (the terms you would actually use or store in your database) for these concepts, 2) start defining the slots and adding constraints, 3) illustrate how to use it with the examples I've gotten from some of you (although I'm still waiting for revisions and could always use more examples!) . I've defined all the classes and have already added a few constraints. The major changes you will see is that I've extended the BiomaterialManipulation a lot and changed terms to be consistent with the Aug 13, 2001 posting of MAGE files on SourceForge. Please realize that this ontology will undoubtedly undergo a number of revisions as we start to put it to use. As always any feedback is appreciated. Cheers, Chris class: BiomaterialDescription class: BiomaterialState instances: biosource, biosample, labeled_extract attribute: has_been_manipulated_by (BiomaterialManipulation) class: BiosourceProperty class: BiosourceProvider attribute: biosource_type (one-of biopsy, paraffin_section) attribute: has_donor (Organization) attribute: has_owner (Person) class: Sex instances: male, female, both_sexes, unknown_sex class: Age attribute: has_measurement (Measurement) attribute: initial_time_point (one-of birth, fertilization, hatching, planting) class: Individual class: BiosourceOntologyEntry superclass: OntologyEntry class: Organism instance: NCBI_taxonomy class: DevelopmentalStage class: OrganismPart class: StrainOrLine class: GeneticVariation class: IndividualGeneticCharacteristics class: DiseaseState class: TargetedCellType class: CellLine class: ClinicalInformation class: BiomaterialManipulation class: BiomaterialPreparation attribute: has_protocol (Protocol) attribute: has_time_of_day (Measurement) attribute: pathological_staging (one-of premortem, postmortem) attribute: biomaterial_amount (Measurement) attribute: biomaterial_purity (range 0-100) class: EnvironmentalHistory class: CultureCondition attribute: has_measurement (Measurement) class: Atmosphere class: Humidity class: Temperature class: Light class: DensityRange class: Generations class: Nutrients attribute: nutrient_compound (Compound) class: ContaminantOrganisms attribute: Is_contaminated_by (Organism) attribute: Is_decontaminated_by (Protocol) class: Host attribute: has_host (Organism) attribute: has_host_part (Organism_part) class: ClinicalHistory attribute: has_clinical_information (ClinicalInformation) attribute: has_lab_values (Measurement) class: PastMedicalHistory class: CurrentDiseaseHistory class: ClinicTreatmentHistory class: FamilyHistory class: Water attribute: has_additives (Compound) attribute: has_treatments (Protocol) class: Bedding class: BarrierFacility attribute: description attribute: rating class: PathogenTests attribute: tested_for (Organism) attribute: result_summary (one-of positive, negative, inconclusive) class: Preservation attribute: preservation_type (one-of seed_dormancy, frozen_storage) attribute: has_protocol (Protocol) class: Treatment attribute: has_protocol (Protocol) class: Modification attribute: modification_type (one-of addition, removal, rearrangement) class: SomaticModification attribute: part_modified (OrganismPart) class: GeneticModification attribute: gene_modified (Gene) class: Starvation attribute: starved_of (Nutrients) class: Infection attribute: infected_by (Organism) class: BehavioralStimulus class: CompoundBasedTreatment attribute: has_compound (Compound) attribute: has_protocol (Protocol) attribute: has_compound_measurement (Measurement) attribute: treatment_application (one-of in_vivo, in_vitro, in_situ) class: Resource class: OntologyEntry attribute: value attribute: description attribute: ID attribute: has_database_entry (DatabaseEntry) class: DatabaseEntry class: Contact class: Organization class: Person class: Compound class: Measurement attribute: value attribute: has_units (Units) class: Units class: Protocol class: Gene ------------------------------ Date: Fri, 31 Aug 2001 10:29:30 +0100 From: Helen Parkinson Subject: [microarray-ontol] Age and dev stage Hi Chris, re the definition of age Definition: The time period elapsed since an identifiable point early in the life of an organism. Examples of the identifiable point include conception, birth, or planting. In some species age is described with ref to some life cycle event (other than birth etc), or developmental stage, I am thinking here of things like parasites and flies. Example: in an adult drosophila the dev stage could be adult and the age 5 days, in this case the age only makes sense in terms of the dev stage adult as the larval age is defined in terms of the larval instars And in eg Leishmania ESTs are divided into promastigote day 3 library, promastigote day 7 library, promastigote day 10 library and amastigote library, It might help to redefine age as measurable from some defined time point in the life cycle, including eg metamorphosis and to specify that point where appropriate what do you think? cheers, Helen Microarray Informatics EBI ------------------------------ Date: Fri, 31 Aug 2001 10:49:30 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] Age and dev stage Helen, Great points. How about this: Definition: The time period elapsed since an identifiable point in the life cycle of an organism. In your larval instar example, "instar" could be the unit of time. I don't know enough about flies to offer an "identifiable point" for when the first larval instar is measured from but I assume there is one isn't there? In regard to parasites, the identifiable point could generically be the beginning of the developmental stage or specifically described for each cycle. I would argue for the generic approach and let the definition of the developmental stage indicate what constitutes the beginning. This generic approach would work for fly larva too I suppose. Thus the definition of Age would be amended as: Definition: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise, the identifiable point must be specified such as planting. The ontology would be amended to: initial_time_point (one-of beginning_of_stage, planting) Is planting the beginning of a developmental stage too?! Other terms to add? Should we allow terms such as: birth, fertilization, hatching even if they are specific cases of beginning_of_stage? Chris On Friday, August 31, 2001, at 05:29 AM, Helen Parkinson wrote: > Hi Chris, > > re the definition of age > > > Definition: The time period elapsed since an > identifiable point early in the life of an organism. > Examples of the identifiable point > include conception, birth, or planting. > > > In some species age is described with ref to some life cycle > event (other than birth etc), or developmental stage, I am > thinking here of things like parasites and flies. > > Example: in an adult drosophila the dev stage could be adult > and the age 5 days, in this case the age only makes sense in > terms of the dev stage adult as > the larval age is defined in terms of the larval instars > > And in eg > > Leishmania ESTs are divided into promastigote > day 3 library, promastigote day 7 library, promastigote day > 10 library and > amastigote library, > > It might help to redefine age as measurable from some > defined time point in the life cycle, including eg > metamorphosis and to specify that point where appropriate > > > what do you think? > > cheers, > > Helen > > Microarray Informatics > EBI > ------------------------------ Date: Mon, 3 Sep 2001 09:33:09 +0100 From: "andy law (RI)" Subject: RE: [microarray-ontol] Age and dev stage All, Sorry, I haven't been paying full attention so this may already have been covered, but... following on from this bit of discussion, is there a way to specify what the units of time are. e.g. in mouse embryo and chick embryo there are defined stages, but in adult life the units might be days, weeks, months or years. If the age is to be defined in relation to a "life-cycle event", the units need also to be defined. Later, Andy > -----Original Message----- > From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] > Sent: 31 August 2001 15:50 > To: Helen Parkinson > Cc: microarray-ontol@ebi.ac.uk > Subject: Re: [microarray-ontol] Age and dev stage > > > Helen, > Great points. How about this: > Definition: The time period elapsed since an identifiable > point in the > life cycle of an organism. > > In your larval instar example, "instar" could be the unit of time. I > don't know enough about flies to offer an "identifiable > point" for when > the first larval instar is measured from but I assume there > is one isn't > there? > > In regard to parasites, the identifiable point could > generically be the > beginning of the developmental stage or specifically > described for each > cycle. I would argue for the generic approach and let the > definition of > the developmental stage indicate what constitutes the beginning. This > generic approach would work for fly larva too I suppose. > > Thus the definition of Age would be amended as: > Definition: The time period elapsed since an identifiable > point in the > life cycle of an organism. If a developmental stage is specified, the > identifiable point would be the beginning of that stage. > Otherwise, the > identifiable point must be specified such as planting. > > The ontology would be amended to: initial_time_point (one-of > beginning_of_stage, planting) > > Is planting the beginning of a developmental stage too?! > Other terms to > add? Should we allow terms such as: birth, fertilization, > hatching even > if they are specific cases of beginning_of_stage? > > Chris > > > On Friday, August 31, 2001, at 05:29 AM, Helen Parkinson wrote: > > > Hi Chris, > > > > re the definition of age > > > > > > Definition: The time period elapsed since an > > identifiable point early in the life of an organism. > > Examples of the identifiable point > > include conception, birth, or planting. > > > > > > In some species age is described with ref to some life cycle > > event (other than birth etc), or developmental stage, I am > > thinking here of things like parasites and flies. > > > > Example: in an adult drosophila the dev stage could be adult > > and the age 5 days, in this case the age only makes sense in > > terms of the dev stage adult as > > the larval age is defined in terms of the larval instars > > > > And in eg > > > > Leishmania ESTs are divided into promastigote > > day 3 library, promastigote day 7 library, promastigote day > > 10 library and > > amastigote library, > > > > It might help to redefine age as measurable from some > > defined time point in the life cycle, including eg > > metamorphosis and to specify that point where appropriate > > > > > > what do you think? > > > > cheers, > > > > Helen > > > > Microarray Informatics > > EBI > > > ------------------------------ Date: Mon, 3 Sep 2001 21:14:45 -0400 From: Chris Stoeckert Subject: Re: [microarray-ontol] Age and dev stage Andy, Units are specified in the Measurement part of Age. Measurement is a MAGE class (see the Measurement.png at http://sourceforge.net/project/showfiles.php?group_id=16076) with Measurement composed of Unit and Unit having the subtypes: TemperatureUnit, MassUnit, VolumeUnit, DistanceUnit, TimeUnit, QuantityUnit, and ConcentrationUnit. Each Unit subtype has a controlled vocabulary (e.g., "years, months, weeks, d, h, m, s, us, other" for TimeUnit). I was thinking of encoding this in our ontology and extending the cv to include "stage." What do you think? Cheers, Chris On Monday, September 3, 2001, at 04:33 AM, andy law (RI) wrote: > All, > > Sorry, I haven't been paying full attention so this may already have > been > covered, but... > > following on from this bit of discussion, is there a way to specify > what the > units of time are. e.g. in mouse embryo and chick embryo there are > defined > stages, but in adult life the units might be days, weeks, months or > years. > If the age is to be defined in relation to a "life-cycle event", the > units > need also to be defined. > > Later, > > Andy > > > >> -----Original Message----- >> From: Chris Stoeckert [mailto:stoeckrt@SNOWBALL.pcbi.upenn.edu] >> Sent: 31 August 2001 15:50 >> To: Helen Parkinson >> Cc: microarray-ontol@ebi.ac.uk >> Subject: Re: [microarray-ontol] Age and dev stage >> >> >> Helen, >> Great points. How about this: >> Definition: The time period elapsed since an identifiable >> point in the >> life cycle of an organism. >> >> In your larval instar example, "instar" could be the unit of time. I >> don't know enough about flies to offer an "identifiable >> point" for when >> the first larval instar is measured from but I assume there >> is one isn't >> there? >> >> In regard to parasites, the identifiable point could >> generically be the >> beginning of the developmental stage or specifically >> described for each >> cycle. I would argue for the generic approach and let the >> definition of >> the developmental stage indicate what constitutes the beginning. This >> generic approach would work for fly larva too I suppose. >> >> Thus the definition of Age would be amended as: >> Definition: The time period elapsed since an identifiable >> point in the >> life cycle of an organism. If a developmental stage is specified, the >> identifiable point would be the beginning of that stage. >> Otherwise, the >> identifiable point must be specified such as planting. >> >> The ontology would be amended to: initial_time_point (one-of >> beginning_of_stage, planting) >> >> Is planting the beginning of a developmental stage too?! >> Other terms to >> add? Should we allow terms such as: birth, fertilization, >> hatching even >> if they are specific cases of beginning_of_stage? >> >> Chris >> >> >> On Friday, August 31, 2001, at 05:29 AM, Helen Parkinson wrote: >> >>> Hi Chris, >>> >>> re the definition of age >>> >>> >>> Definition: The time period elapsed since an >>> identifiable point early in the life of an organism. >>> Examples of the identifiable point >>> include conception, birth, or planting. >>> >>> >>> In some species age is described with ref to some life cycle >>> event (other than birth etc), or developmental stage, I am >>> thinking here of things like parasites and flies. >>> >>> Example: in an adult drosophila the dev stage could be adult >>> and the age 5 days, in this case the age only makes sense in >>> terms of the dev stage adult as >>> the larval age is defined in terms of the larval instars >>> >>> And in eg >>> >>> Leishmania ESTs are divided into promastigote >>> day 3 library, promastigote day 7 library, promastigote day >>> 10 library and >>> amastigote library, >>> >>> It might help to redefine age as measurable from some >>> defined time point in the life cycle, including eg >>> metamorphosis and to specify that point where appropriate >>> >>> >>> what do you think? >>> >>> cheers, >>> >>> Helen >>> >>> Microarray Informatics >>> EBI >>> >> > ------------------------------ Date: Tue, 04 Sep 2001 11:13:43 +0100 From: Helen Parkinson Subject: [Fwd: Re: [microarray-ontol] Age and dev stage] Hi Chris, my local parasite expert says that the generic way will work fine for parasites. In flies the larvae are classified according to dev stage as age is relative - a population reared @ 25 deg C will be a different age but could be at the same dev stage as a population reared at 18 deg C. This example makes me think that dev stage is more informative than age in many cases and that age should always be quoted ref. to dev stage if possible, with appropriate units from measurement. I don't know if you could call planting a dev stage but I have seen terms in EMBL such as: dev_stage="15 days post planting" again what this actually means would depend upon conditions of growth so if it could be expressed in terms of dev stage instead it would be more informative. This is probably an inaccurate use of dev_stage though. I think the definition is fine: > Thus the definition of Age would be amended as: > Definition: The time period elapsed since an identifiable point in the > life cycle of an organism. If a developmental stage is specified, the > identifiable point would be the beginning of that stage. Otherwise, the > identifiable point must be specified such as planting. possible definition of life cycle: life cycle - the various developmental stages that an individual species passes through to maturity might be useful to include that somewhere on the pages. Also dev_stage can be defined as part of a life cycle, so that could also be added to the ontology Adding stage to the cv is a good idea too, cheers Helen Chris Stoeckert wrote: > > Helen, > Great points. How about this: > Definition: The time period elapsed since an identifiable point in the > life cycle of an organism. > > In your larval instar example, "instar" could be the unit of time. I > don't know enough about flies to offer an "identifiable point" for when > the first larval instar is measured from but I assume there is one isn't > there? > > In regard to parasites, the identifiable point could generically be the > beginning of the developmental stage or specifically described for each > cycle. I would argue for the generic approach and let the definition of > the developmental stage indicate what constitutes the beginning. This > generic approach would work for fly larva too I suppose. > > Thus the definition of Age would be amended as: > Definition: The time period elapsed since an identifiable point in the > life cycle of an organism. If a developmental stage is specified, the > identifiable point would be the beginning of that stage. Otherwise, the > identifiable point must be specified such as planting. > > The ontology would be amended to: initial_time_point (one-of > beginning_of_stage, planting) > > Is planting the beginning of a developmental stage too?! Other terms to > add? Should we allow terms such as: birth, fertilization, hatching even > if they are specific cases of beginning_of_stage? > > Chris > > On Friday, August 31, 2001, at 05:29 AM, Helen Parkinson wrote: > > > Hi Chris, > > > > re the definition of age > > > > > > Definition: The time period elapsed since an > > identifiable point early in the life of an organism. > > Examples of the identifiable point > > include conception, birth, or planting. > > > > > > In some species age is described with ref to some life cycle > > event (other than birth etc), or developmental stage, I am > > thinking here of things like parasites and flies. > > > > Example: in an adult drosophila the dev stage could be adult > > and the age 5 days, in this case the age only makes sense in > > terms of the dev stage adult as > > the larval age is defined in terms of the larval instars > > > > And in eg > > > > Leishmania ESTs are divided into promastigote > > day 3 library, promastigote day 7 library, promastigote day > > 10 library and > > amastigote library, > > > > It might help to redefine age as measurable from some > > defined time point in the life cycle, including eg > > metamorphosis and to specify that point where appropriate > > > > > > what do you think? > > > > cheers, > > > > Helen > > > > Microarray Informatics > > EBI > > ------------------------------ Date: Tue, 4 Sep 2001 14:47:17 -0400 From: Chris Stoeckert Subject: Re: [Fwd: Re: [microarray-ontol] Age and dev stage] - --Apple-Mail-28289410-3 Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset=us-ascii Helen, > I think the definition is fine: >> Thus the definition of Age would be amended as: >> Definition: The time period elapsed since an identifiable point in the >> life cycle of an organism. If a developmental stage is specified, the >> identifiable point would be the beginning of that stage. Otherwise, the >> identifiable point must be specified such as planting. Great. I will amend the one on the web page and in the ontology. > possible definition of life cycle: > > life cycle - the various developmental stages that an > individual species > passes through to maturity > > might be useful to include that somewhere on the pages. Also > dev_stage can be defined as part of a life cycle, so that > could also be added to the ontology Will need to think more about this. We've put organism-specific terms such as those related to developmental stage under BiosourceOntologyEntry to point to external ontologies however if there are generic terms that can apply across many (not necessarily all) species we could create a LifeCycle class under BiosourceProperty. Is that what you were thinking? > Adding stage to the cv is a good idea too, OK will do. What about including these terms such as "birth, fertilization, hatching" for those people not using developmental stages from a well-defined source? For example, a blood sample from a 46-year old adult male might be annotated as "adult" for developmental stage without specifying an existing ontology/vocabulary and "birth" would be used as the identifiable point. As I indicated above, we can also start creating controlled vocabularies for common terms. Cheers, Chris - --Apple-Mail-28289410-3 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=us-ascii Helen, I think the definition is fine: Thus the definition of Age would be amended as: Definition: The time period elapsed since an identifiable point in the life cycle of an organism. If a developmental stage is specified, the identifiable point would be the beginning of that stage. Otherwise, the identifiable point must be specified such as planting. Great. I will amend the one on the web page and in the ontology. 0000,0000,DEB7 possible definition of life cycle: life cycle - the various developmental stages that an individual species passes through to maturity might be useful to include that somewhere on the pages. Also dev_stage can be defined as part of a life cycle, so that could also be added to the ontology Will need to think more about this. We've put organism-specific terms such as those related to developmental stage under BiosourceOntologyEntry to point to external ontologies however if there are generic terms that can apply across many (not necessarily all) species we could create a LifeCycle class under BiosourceProperty. Is that what you were thinking? 0000,0000,DEB7 Adding stage to the cv is a good idea too, OK will do. What about including these terms such as "birth, fertilization, hatching" for those people not using developmental stages from a well-defined source? For example, a blood sample from a 46-year old adult male might be annotated as "adult" for developmental stage without specifying an existing ontology/vocabulary and "birth" would be used as the identifiable point. As I indicated above, we can also start creating controlled vocabularies for common terms. Cheers, Chris= - --Apple-Mail-28289410-3-- ------------------------------ Date: Wed, 05 Sep 2001 11:01:19 +0100 From: Helen Parkinson Subject: Re: [Fwd: Re: [microarray-ontol] Age and dev stage] Chris, re: life cycle, under the BiosourceOntologyEntry dev_stage is a class, but dev_stage is a part of life cycle and the ontology doesn't reflect that, that's what I was getting at. I don't think there is any need to have life cycle as a class of BiosourceProperty, I think use of a set of general terms there would just be confusing. Using terms such as birth, hatching etc makes perfect sense to me, many users will not need the species specific stuff, cheers Helen Chris Stoeckert wrote: > > Helen, > > I think the definition is fine: > > Thus the definition of Age would be amended as: > Definition: The time period elapsed since an identifiable point in the > life cycle of an organism. If a developmental stage is specified, the > identifiable point would be the beginning of that stage. Otherwise, the > identifiable point must be specified such as planting. > > Great. I will amend the one on the web page and in the ontology. > > possible definition of life cycle: > > life cycle - the various developmental stages that an > individual species > passes through to maturity > > might be useful to include that somewhere on the pages. Also > dev_stage can be defined as part of a life cycle, so that > could also be added to the ontology > > Will need to think more about this. We've put organism-specific terms such as those related to developmental stage under BiosourceOntologyEntry to point to external ontologies however if there are generic terms that can apply across many (not necessarily all) species we could create a LifeCycle class under BiosourceProperty. Is that what you were thinking? > > Adding stage to the cv is a good idea too, > > OK will do. What about including these terms such as "birth, fertilization, hatching" for those people not using developmental stages from a well-defined source? For example, a blood sample from a 46-year old adult male might be annotated as "adult" for developmental stage without specifying an existing ontology/vocabulary and "birth" would be used as the identifiable point. As I indicated above, we can also start creating controlled vocabularies for common terms. > > Cheers, > Chris ------------------------------ End of microarray-ontol-digest V1 #11 *************************************