W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2014

Re: hcls dataset description comments--Dataset Descriptions vs. PROV

From: Stian Soiland-Reyes <soiland-reyes@cs.manchester.ac.uk>
Date: Thu, 28 Aug 2014 00:47:58 +0100
Message-ID: <CAPRnXtm3yeJsjvnewAzqTtFMUkoAje1tAnp7Hkgo4DZBBxwtig@mail.gmail.com>
To: Michael Miller <Michael.Miller@systemsbiology.org>
Cc: Alasdair J G Gray <A.J.G.Gray@hw.ac.uk>, w3c semweb hcls <public-semweb-lifesci@w3.org>, "pav-ontology@googlegroups.com" <pav-ontology@googlegroups.com>
That is a nice use-case.

If you make a new file by selecting out a column from a single source file,
that is a narrow case of pav:importedFrom in my opinion. This is why we
added in http://purl.org/pav/html#http://purl.org/pav/importedFrom the
phrase:

> The imported resource does not have to be complete, but should be
consistent with the knowledge conveyed by the original resource.

e.g. if you extract a list of all the names and  email addresses from an
address book (but skipping phone and fax numbers) then that is still a case
of import (which is not complete, but consistent).

However if you do anything "clever", like importing only those addresses
that are in the UK, then you are deriving new information and cannot use
pav:importedFrom (pav:derivedFrom would be appropriate).


In your case you are turning it around across multiple sources.. so if I
understand it right, it is as if your source is a set of vcard files, one
per person, and then you create new files, one that has all the email
addresses, another one with all the names, etc. I don't think it should
matter if the 'subject' is in the column or the row.

The new resource is one that is expressing a collection of email addresses.
So if we are to express an pav:importedFrom here, it should better go to
some collection of vcards, rather than multiple imports of many vcard files
(where did that list of vcard files come from? Who decides which is in or
out?)

So I think it sounds like it would be better to express that you are
importing the collection/aggregation of those files (e.g. an
ore:Aggregation) - rather than having hundred import edges. Then you have a
resource to describe where that selection of files came from rather then
them seemingly randomly meeting up in that import. :-)

e.g.


@base <http://www.example.com/>

<merged.csv> pav:importedFrom <sourcefiles/> ;
  pav:importedBy <http://orcid.org/0000-0001-9842-9718> ;
  pav:createdWith </merger-tool> .

<sourcefiles/> a ore:Aggregation ;
  ore:aggregates <sourcefiles/file1.csv>, <sourcefiles/file2.csv>,
<sourcefiles/file3.csv> ;
  pav:createdBy <http://orcid.org/0000-0001-9842-9718> ;
  pav:derivedFrom <https://tcga-data.nci.nih.gov/tcga/is-there-a-query-link>
;
  pav:providedBy <https://tcga-data.nci.nih.gov/tcga/> .

<sourcefiles/file1.csv> pav:retrievedFrom <
https://tcga-data.nci.nih.gov/tcga/was-there-a-download-link> ;
   pav:createdWith <https://tcga-data.nci.nih.gov/tcga/> .

<http://orcid.org/0000-0001-9842-9718> a foaf:Person, prov:Person;
   foaf:name "Stian Soiland-Reyes" .



For argument's sake I have stayed with PAV properties here as I think it
makes it rather clear. The above says that the <merged.csv> conveys the
same knowledge as the <sourcefiles/> aggregation which its content is
imported from. The CSV representation was made with /merger-tool. Stian
initiated the import - clicked the button so to speak (perhaps set some
parameters) - but did not (according to these statements alone) convey any
knowledge into the CSV.

The ORE aggregation (but not its files) was created by Stian. (but I didn't
author/contribute to the aggregation, unless I selected the files). It
contains 3 files. If there is a query link, then we can give its
pav:derivedFrom (or even pav:importedFrom) - but anyway we can give at
least pav:providedBy to indicate the original publisher of this collection
(e.g. the list was on the result page).

Each of the files have been retrieved - now if there is not a download-link
from tcga this gets a bit tricky, but again pav:providedBy can be a last
resort to at least indicate the service. Here we use pav:createdWith - I
don't know about the provenance of those files, are they verbatimly
uploaded to tcga (just pav:providedBy) or created on demand based on the
query (pav:createdWith)?




On 21 August 2014 16:21, Michael Miller <Michael.Miller@systemsbiology.org>
wrote:

> 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.
>



-- 
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
Received on Wednesday, 27 August 2014 23:48:47 UTC

This archive was generated by hypermail 2.4.0 : Friday, 17 January 2020 17:21:41 UTC