- From: Michael Miller <Michael.Miller@systemsbiology.org>
- Date: Thu, 21 Aug 2014 08:21:05 -0700
- To: Stian Soiland-Reyes <soiland-reyes@cs.manchester.ac.uk>, Alasdair J G Gray <A.J.G.Gray@hw.ac.uk>
- Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>
- Message-ID: <187bf7ae948255167d52c4c1789535e0@mail.gmail.com>
hi stian and alasdair, there's a real use case along these lines that is part of the broad's TCGA firehose pipeline[1]. for each tumor type and for each of the platforms (gene expression, miRNA, methylation, etc.) the data is stored per subject[2]. part of the broad pipeline 'merges' all the values from the subject files into one file per column from the set of original files per subject. so for miRNA[3], there is a file that merges all the raw values, a file that merges all the RPKM values, and a file that merges the values from the cross-mapping column. the gene names are not duplicated, they are the row headers. so no values are changed, just a bit of modest reformatting and filtering. cheers, michael Michael Miller Software Engineer Institute for Systems Biology [1] https://confluence.broadinstitute.org/display/GDAC/Dashboard-Stddata [2] https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp and https://tcga-data.nci.nih.gov/ccg-data-web/searchForTCGAData.htm [3] http://gdac.broadinstitute.org/runs/stddata__2014_07_15/data/STAD/20140715/ and the file gdac.broadinstitute.org_STAD.Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2014071500.0.0.tar.gz <http://gdac.broadinstitute.org/runs/stddata__2014_07_15/data/STAD/20140715/gdac.broadinstitute.org_STAD.Merge_mirnaseq__illuminaga_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data.Level_3.2014071500.0.0.tar.gz> *From:* stian@mygrid.org.uk [mailto:stian@mygrid.org.uk] *On Behalf Of *Stian Soiland-Reyes *Sent:* Wednesday, August 20, 2014 5:46 PM *To:* Alasdair J G Gray *Cc:* w3c semweb hcls; Joachim Baran; Michael Miller *Subject:* Re: hcls dataset description comments--Dataset Descriptions vs. PROV Hi, sorry for not replying earlier. I think it depends on the nature of the concatenation. pav:importedFrom with multiple resources would only make sense for 'pure' concatenation where no additional knowledge is conceived, and the content of both sources can be said to be preserved. So for instance, if two CSV files are simply merged by adding the new rows at the bottom, it could work with multiple pav:importedFrom. Anything more clever that goes beyond just changing formats, like matching up foreign keys or heuristic matching on compound names would mean you are adding new content/knowledge and must use pav:derivedFrom instead. Concatenating RDF graphs is a grey area here, as nodes with the same URI automatically merge. Perhaps it also depends on your reason for adding the second source - was that based on inspecting the first resource (e.g. following links) or just something you always do blindly? So given that pav:importedFrom with multiple sources is a thin line that can be hard to explain, perhaps it's better to just leave the above as an unexplored edge-case, and rather recommend using pav:derivedFrom (or the non-specific prov:wasDerivedFrom) when there are multiple sources. On 11 Aug 2014 15:53, "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk> wrote: Hi Stian, On 5 Aug 2014, at 13:37, Stian Soiland-Reyes < soiland-reyes@CS.MANCHESTER.AC.UK> wrote: Just some inputs: PROV defines prov:wasDerivedFrom which in broad sense describes such a relationset between datasets. However you do not know anything more about what kind of derivation we are talking about. In PAV we found the need to specialize three types of derivation: pav:retrievedFrom - http://purl.org/pav/html#http://purl.org/pav/retrievedFrom .. a byte-for-byte download pav:importedFrom - http://purl.org/pav/html#http://purl.org/pav/importedFrom .. a somewhat equivalent form of the source, but after some kind of transformation or selection (e.g. CSV -> XML) pav:derivedFrom - http://purl.org/pav/html#http://purl.org/pav/derivedFrom .. when the new resource has been further refined or modified (somewhat adding additional knowledge) If you are simply concatenating several dataset, then multiple pav:importedFrom statements would make sense. If further knowledge is added, say by reasoning or calculation, then pav:derivedFrom would make sense. Are you sure about this? I thought that pav:importedFrom meant that the derived dataset was essentially the same data as the original modulo data format, i.e. it is a 1:1 relationship (as near as possible). To my mind, this would mean that you could not have more than one pav:importedFrom statement for a dataset. Alasdair Now if you want to detail exactly how those datasets have been combined, I think you are right that would make sense to break down the derivation using PROV statements, e.g. a series of activities, generation and usage. How to describe these activities (e.g. subclasses and properties) will be specific to each case. If the process you generated the dataset with somewhat resembles a dataflow, you might be interested in the wfprov and wfdesc ontologies that specialize PROV to define a WorkflowRun of steps of ProcessRuns, which can be related to a common workflow description (e.g. a prov:Plan): http://purl.org/wf4ever/model#wfprov OPMW is a similar approach: http://www.opmw.org/model/OPMW/ On 4 August 2014 17:44, Michael Miller <Michael.Miller@systemsbiology.org> wrote: hi all, as you are all undoubtedly aware, a major, if not the major TCGA dataset use cases revolve around taking the 3rd level data from the TCGA dcc repository and doing analysis, producing 4th level data such as clusters, pca, etc. one of the things we do here at ISB is produce an intermediate data step that combines the different platforms (mRNA, miRNA, RPPA, METH, etc.) into one feature matrix so that the analysis can use all the platforms together. the Broad firehose pipeline also has this as one of its outputs. as some of my comments allude to, it doesn't seem that Dataset Descriptions deal with the use case of describing a dataset that is specifically derived from other datasets, which is what we are looking at ways we might describe our data when we publish it. i took a look at PROV and, i've got a bit more mapping to do, but it seems like PROV provides the terms we need. but this has lead me to ask the question of what is the relation of Dataset Descriptions and PROV and how should they/should they be used together? i think the above use case is quite common for datasets being published so might deserve a discussion in the Dataset Descriptions note cheers, michael Michael Miller Software Engineer Institute for Systems Biology From: Joachim Baran [mailto:joachim.baran@gmail.com] Sent: Thursday, July 31, 2014 3:43 PM To: Michael Miller Cc: w3c semweb hcls Subject: Re: hcls dataset description comments Hi! I will ponder about your edit suggestion of your first bullet point. I am not sure at the moment if it would have wider implications. You are right that the use cases were written by the groups themselves. I do not know how to improve the use cases without rewriting them, which might not be agreeable to all parties involved. C'est la vie. The role of Data Catalogs should then be discussed during out next conf call. Thanks for highlighting that this might be unclear to readers. Kim On 30 July 2014 10:41, Michael Miller <Michael.Miller@systemsbiology.org> wrote: hi kim, 'For other edits, please fork the repository and create a pull request with your changes' of the four general comments, the first is really the only 'edit', i didn't put it in the minor edits because it had some implications that the group might not agree with. if the change makes sense, it might be easier for you to make the edit. the other three are general comments and i'm not sure what the solution might be, they were mainly points, as a reader, that weren't clear or were a bit confusing. these were all from the use case section so were probably written by the groups themselves? if i have permission, i can certainly add them as issues. cheers, michael Michael Miller Software Engineer Institute for Systems Biology From: Joachim Baran [mailto:joachim.baran@gmail.com] Sent: Tuesday, July 29, 2014 11:56 AM To: Michael Miller Cc: w3c semweb hcls Subject: Re: hcls dataset description comments Hi! Thanks for the suggestions. I have incorporated your minor edits. Unbelievable how those slipped through after so many re-readings still. For other edits, please fork the repository and create a pull request with your changes. Best wishes, Kim On 23 July 2014 08:53, Michael Miller <Michael.Miller@systemsbiology.org> wrote: hi kim, thanks for the pointer, i've updated my comments based on this newer draft below. many fewer and i especially like the complete example in 10.1! cheers, michael Michael Miller Software Engineer Institute for Systems Biology general comments: · s4.4 'Dataset Linking': might mention also that datasets are derived from other datasets? 'A dataset may incorporate, or link to, data in other datasets, e.g. in the creation of a data mashup ' --> 'A dataset may incorporate, be derived from, or link to, data in other datasets, e.g. in the analysis of original datasets or in the creation of a data mashup ' · s8: odd that some of the top sections (8.1-8.3,8.5-8.7) are individual organizations but three (8.4, 8.8, 8.9) have subsections for different organizations. maybe organize so all top level sections define a type of organization with subsections beneath or make all top-level? · s8: some of the use cases could be more focused on how this note will help them (8.5-8.7) · s8.9: how do Data Catalogs fit into this note? wasn't clear to me how this note is relevant to them our use case questions: · how to reference 3rd party datasets that aren't described by this standard, i.e. TCGA data from the DCC, simply use 'pav:retrievedFrom' with the IRI being the URL into the repository? · we have a lot of intermediary files that we won't publish, the software specified in creating our published datasets from its sources form a (branching) workflow with the input being from the previous step(s) in the workflow. how best to represent this? this note doesn't seem to cover how the dataset is created so any recommendations? minor edits: · there are two s6.2.3 sections · s8.8.1: '... what period it is updated. To know when to...' should be '...what period it is updated to know when to...'? From: Joachim Baran [mailto:joachim.baran@gmail.com] Sent: Tuesday, July 22, 2014 3:43 PM To: Michael Miller Cc: w3c semweb hcls Subject: Re: hcls dataset description comments Hello, I believe you were looking at an old document. There is currently only one Figure in the note. Please check the actual draft at: http://htmlpreview.github.io/?https://github.com/joejimbo/HCLSDatasetDescriptions/blob/master/Overview.html Best wishes, Kim On 22 July 2014 15:36, Michael Miller <Michael.Miller@systemsbiology.org> wrote: hi all, tremendous work, very clear and well-written. my group at ISB, the Shmulevich lab is looking to provide provenance for the analysis datasets we are producing for TCGA. we're not sure if we'll be able to 'go all the way' but we want to make sure we have at hand all the information that we could, at least in theory, be compliant. as long as i was reading the document, below are some notes. general comments: · s4.4 'Dataset Linking': might mention also that datasets are derived from other datasets? 'A dataset may incorporate, or link to, data in other datasets, e.g. in the creation of a data mashup ' --> 'A dataset may incorporate, be derived from, or link to, data in other datasets, e.g. in the analysis of original datasets or in the creation of a data mashup ' · the chembl example in s5 is not compliant to the property table below, it probably is only supposed to show the relationship of the three terms but that could be clarified · s6.2.12 could use the example filled in · 6.3.2: not sure what an 'X level description' is · s8: odd that some of the top sections (8.1-8.3,8.5-8.7) are individual organizations but three (8.4, 8.8, 8.9) have subsections for different organizations. maybe organize so all top level sections define a type of organization with subsections beneath or make all top-level? · s8: many of the use cases could be more focused on how this note will help them · s8.9: how do Data Catalogs fit into this note? wasn't clear to me how this note is relevant to them · would be nice to have a 'complete' example p[put together, maybe based on chembl? our use case questions: · how to reference 3rd party datasets that aren't described by this standard, i.e. TCGA data from the DCC, simply use 'pav:retrievedFrom' with the IRI being the URL into the repository? · we have a lot of intermediary files that we won't publish, the software specified in creating our published datasets from its sources form a (branching) workflow with the input being from the previous step(s) in the workflow. how best to represent this? this note doesn't seem to cover how the dataset is created so any recommendations? text issues: · Figure 1: 'Overview of dataset description level metadata profiles and their relationships': reference not resolved, image doesn't show · Figure 2: 'Improve diagram. Multiple appearance of concepts/description levels unclear.': reference not resolved, image doesn't show. add actual label minor edits: · bottom of s.3: 'placeholde' should be 'placeholder' · use straight quotes rather than slant quotes in s6.2.2 example (and elsewhere)? · the text runs out of the box in s6.2.3 'Description' · s6.2.3: 'Dates of Creation and Issuance': 'state the date the dataset was generated using dct:created and/or the date the dataset was made public using dct:created' should be 'state the date the dataset was generated using dct:created and/or the date the dataset was made public using dct:issued'? · there are two s6.2.3 sections · s6.2.4: 'Creation: ... The date of authorship' should be '...The date of creation' and 'Curation:... The date of authorship' should be '...The date of curation'? · s8.5: the author list has end parenthesis without beginning parenthesis · s8.8.1: '... what period it is updated. To know when to...' should be '...what period it is updated to know when to...' cheers, michael Michael Miller Software Engineer Institute for Systems Biology -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester http://soiland-reyes.com/stian/work/ http://orcid.org/0000-0001-9842-9718 Alasdair J G Gray Lecturer in Computer Science, Heriot-Watt University, UK. Email: A.J.G.Gray@hw.ac.uk Web: *MailScanner has detected a possible fraud attempt from "www.macs.hw.ac.uk" claiming to be* http://www.alasdairjggray.co.uk <http://www.macs.hw.ac.uk/~ajg33> ORCID: http://orcid.org/0000-0002-5711-4872 Telephone: +44 131 451 3429 Twitter: @gray_alasdair ------------------------------ Sunday Times Scottish University of the Year 2011-2013 Top in the UK for student experience Fourth university in the UK and top in Scotland (National Student Survey 2012) We invite research leaders and ambitious early career researchers to join us in leading and driving research in key inter-disciplinary themes. Please see www.hw.ac.uk/researchleaders for further information and how to apply. Heriot-Watt University is a Scottish charity registered under charity number SC000278.
Received on Thursday, 21 August 2014 15:21:38 UTC