Helen Parkinson
Fri, 24 Jul 2009 14:45:54 -0700
HiI meant to comment on this, I would not attempt a mage-ml->RDF transform, I can probably do something more quickly with an rdf export n of transformed data analysed for over/under expressions plus factor values and genes and we'll have a student to work on this I hope
Helen Miller, Michael D (Rosetta) wrote:
hi kei and helen, like helen, i've been following the HCLS working groups with great interest. as one of the designers, with helen, of the MAGE-ML and MAGE-TAB specs i might be able to provide a little technical insight into the formats. (from helen)"This is probably as we don't have data - here's a list of human experiments with the term neuron - if any of these are useful, then I can prioritize their curation and inclusion in an atlas release"kei, are the NIH Neuroscience Microarry Consortium exeriments you've cited and others like them in GEO or ArrayExpress? a set of those could be a good starting point for helen. first, MAGE-ML is based on a DTD[1], not an XSD. in early 2002 as the OMG Gene Expression specification[1] was being finalized, XSD was still in its infancy so we weren't comfortable at that point generating a XSD. the MAGE-OM UML[2], in a very early XMI format from Rational Rose andUniSys, was used to generate the DTD with code we wrote ourselves[3].the UML model was designed to capture the flow of a microarray experiment and how the resulting arrays were organized in the experiment based on how the samples were treated and/or on the samples' phenotypes for the purpose of a reviewer understanding the methodology and for aresearcher replicating and/or re-analyzing the results.some of the details of the flow may not be of much interest, i.e. it might be worth simply connecting the BioSource elements with their gene expression data and not worrying about how the hybridization was performed. but that depends on what you want to do and you know that better than i. also, the data itself are specified in external files, typically in a white-space delimited format where the column headers are specified in the MAGE-ML file in the QuantitationTypeDimension element and the identifiers of the row specified in one of the three DesignElementDimension elements, Feature, Reporter, CompositeSequence, depending on how derived the data is. Also the data can be in a vendor specific format such as the Affymetrix CEL (since the CEL file internally specifies the dimensions often they are left out of the MAGE-ML document). the ExperimentalFactor elements are certainly relevant and if you've looked at some of the examples you will noticed that the BioSource elements, in particular, and other elements are annotated by OntologyEntry elements. from the gene expression specification: "OntologyEntry A single entry from an ontology or a controlled vocabulary. For instance, category could be 'species name,' value could be 'homo sapiens' and ontology would be taxonomy database, NCBI." for the element an ontology entry element is annotating, we looked at it as a way of specifying something like "the object identified by the element is an instance of the class/individual specified by the OntologyEntry" so from "kitm-affy-droso-176167" one sees that the BioSource is an "instance of" Drosophila, whole animal, whole head and an age of 3 days: <BioSource identifier="arrayconsortium.tgen.org::biosource.181527" name="Oregon R head 3d"> <Characteristics_assnlist> <OntologyEntry category="Organism" value="Drosophila" description="Drosophila"> <OntologyReference_assn> <DatabaseEntry accession="#Organism" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#Organism";> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> <!-- snip --> </OntologyReference_assn> </OntologyEntry> <OntologyEntry category="OrganismPart" value="whole animal" description=""> <OntologyReference_assn> <DatabaseEntry accession="#OrganismPart" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#OrganismPar t"> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <!-- snip --> </OntologyEntry> <OntologyEntry category="OrganismPartRegion" value="whole head" description=""> <!-- snip --> </OntologyEntry> <!-- snip --> <OntologyEntry category="Age" value="Age"> <OntologyReference_assn> <DatabaseEntry accession="#Age" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#Age";> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category="has_measurement" value="has_measurement"> <OntologyReference_assn> <DatabaseEntry accession="#has_measurement" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#has_measure ment"> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category="Measurement" value="Measurement"> <OntologyReference_assn> <DatabaseEntry accession="#Measurement" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#Measurement "> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category="has_value" value="has_value"> <OntologyReference_assn> <DatabaseEntry accession="#has_value" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#has_value";> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category="has_value" value="3"/> </Associations_assnlist> </OntologyEntry> <OntologyEntry category="has_units" value="has_units"> <OntologyReference_assn> <DatabaseEntry accession="#has_units" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#has_units";> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> <Associations_assnlist> <OntologyEntry category="TimeUnit" value="days" description="24 hours, time unit"> <OntologyReference_assn> <DatabaseEntry accession="#days" URI="http://mged.sourceforge.net/ontologies/MGEDontology.php#days";> <Database_assnref> <Database_ref identifier="MO"/> </Database_assnref> </DatabaseEntry> </OntologyReference_assn> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> </Associations_assnlist> </OntologyEntry> <!-- snip --> </Characteristics_assnlist> <!-- snip --> </BioSource> by the by, the MAGE-ML examples i've looked at from the NIH Neuroscience Microarry Consortium are not in a valid MAGE-ML.dtd format. i'll send a follow-up e-mail dealing with the problems i see. they are not far off but are invalid in a number of places. cheers, michael Michael Miller Lead Software Developer Rosetta Biosoftware Business Unit www.rosettabio.com [1] http://www.omg.org/spec/GENE/1.1/ (sadly, the original links to the MAGEstk appear to be broken, this mirror site still has the MAGE related files built up over the years, here's my best guess as to the most helpful for the references) [2] http://www.mirrorservice.org/sites/download.sourceforge.net/pub/sourcefo rge/m/mg/mged/ v1.0: http://www.mirrorservice.org/sites/download.sourceforge.net/pub/sourcefo rge/m/mg/mged/MAGE-2002-01-07.xmi.gz/MAGE-2002-01-07.xmi v1.1: http://www.mirrorservice.org/sites/download.sourceforge.net/pub/sourcefo rge/m/mg/mged/MAGE.xmi.gz[peek] [3] http://www.mirrorservice.org/sites/download.sourceforge.net/pub/sourcefo rge/m/mg/mged/MAGE%20Java%20API/20010911/-----Original Message-----From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-lifesci-requ...@w3.org] On Behalf Of Helen ParkinsonSent: Wednesday, July 22, 2009 2:55 AM To: Kei Cheung Cc: HCLS; James Malone Subject: Re: BioRDF Telcon Responses in line.curated it and1. We have text mined much of the Affymetrix GEO data,running QC acrossimported it into ArrayExpress - there is now much better sample annotation than the native data in GEO. We also areannotation andall the data files so we know which should be excluded for future analyses.I think it's the right thing to do both to enrich datacase(s) toto enhance data quality. This will help data integration a lot.Currently, we are exploring query federation in the neuroscience context. It'd be great if we can use the neuroscience usehelp drive your ontology development for text mining and data visualization. In addition to the NIH neuroscience microarray consortium, it may be possible to collaborate with the Neuroscience Information Framework (NIF) to see if we can utilize some of its resources (e.g., neuron ontology).Re-use of the neuron ontology is possible, but it depends on whether there is available data to annotate either in ArrayExpress or GEO. If you can get me a list of experiments accessions or pubmed ids I can see if this is feasible~30,000 hybs3. We have summary level data of genes x conditions forindicatingworth of data in our gene expression atlas with p valuesinterest.relative under/over-expression. We are planning to export these as triples as soon as we publish the atlas - these may be ofof gene listwww.ebi.ac.uk/gxa - there's an API at present, but it will be improved in the next month or so.It fits well with what we're currently exploring in termsrepresentation and linking genes and samples to existingontologies.It'd be great if we can download or fetch RDF triples fromEBI atlas.We have a student starting work on this in a month, if you can produce concrete use cases for how you want to access these data we can do something.do a themed4. If neuroscience data is of specific interest we couldor projectatlas release where we add datasets for a given communityArrayExpress orand make these available. These can be identified byattributesGEO accession or pubmed and we can re-annotate the genes vs Uniprot/Ensembl, add GO terms, etc and curate the sampleplace asand experimental variables. These pipelines are already inneuro-atlas). II think it's a great idea to do a themed atlas (e.g.,part of our production workflow.just played with gxa a little bit. It's nice! For example, I could find genes that are over-expressed in the hippocampus brain region across different experiments. However, when I tried to do the same thing for neurons, there are only a few neuron types that I can select. It'd be nice if we can have more neuron types, for instance.This is probably as we don't have data - here's a list of human experiments with the term neuron - if any of these are useful, then I can prioritise their curation and inclusion in an atlas releasehttp://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=neuron&species=Homo+sapiens&array=&exptype=&pagesize=25> &sortby=releasedate&sortorder=descendingand brain http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=brain&species=Homo+sapiens&array=&exptype=&pagesize=25> &sortby=releasedate&sortorder=descendinguse our data,I'd be very happy to collaborate, and for this group toplease let mewe spend a lot of time adding semantic value to it, socollaborationWe are also looking into the possibility of establishingknow if this is of interestwith the scientific discourse task force based on themicroarray usecase. We're planning to have a microarray-related presentation and discussion on Aug. 31 (Monday, 11 am EDT/5 pm CET). Details will be announced later. It'd be great if you can join the BioRDF call to participate in the discussion.Cheers, -Keibest regards Helen Kei Cheung wrote:The minutes for yesterday's BioRDF call are available at:http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009-07-20_Conference_CalltranscriptThanks to Lena for scribing and Eric for retrieving thebe held atfrom the IRC log. Cheers, -Kei Kei Cheung wrote:This is a reminder that the next BioRDF teleconf. willmicroarray use11 am EDT (5 pm CET) on Monday, July 20 (see details below).I created the following wiki page for discussing thedetails, or seecase: http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2 Cheers, -Kei == Conference Details == * Date of Call: Monday July 20, 2009 * Time of Call: 11:00 am Eastern Time * Dial-In #: +1.617.761.6200 (Cambridge, MA) * Dial-In #: +33.4.89.06.34.99 (Nice, France) * Dial-In #: +44.117.370.6152 (Bristol, UK) * Participant Access Code: 4257 ("HCLS")* IRC Channel: irc.w3.org port 6665 channel #hcls (see [http://www.w3.org/Project/IRC/ W3C IRC page] for[http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC]) * Duration: ~1 hour * Frequency: bi-weekly * Convener: Kei Cheung == Agenda == * Roll call and introduction (Kei) * TCM data quick update (Jun, Kei) * Query federation use case expanison (microarray) (All)-- Helen Parkinson, PhD ArrayExpress Production Coordinator,Microarray Informatics Team, EBIEBI 01223 494672 Skype: helen.parkinson.ebi