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

From: Melissa Haendel <haendel@ohsu.edu>
Date: Mon, 4 Aug 2014 16:56:29 +0000
To: Michael Miller <Michael.Miller@systemsbiology.org>
CC: Joachim Baran <joachim.baran@gmail.com>, w3c semweb hcls <public-semweb-lifesci@w3.org>
Message-ID: <E89DEE68-1967-411A-9BB3-A43A3BB619F8@ohsu.edu>
Hi all,
I agree Michael, and I had put a note to this effect on the original google doc.
We deal with the same issue all the time, and ideally we'd be able to automate the display of the provenance chain if such a thing were specified well enough.

Cheers,
Melissa


On Aug 4, 2014, at 9:44 AM, Michael Miller <Michael.Miller@systemsbiology.org<mailto: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<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<mailto: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<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<mailto: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<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<mailto: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







Dr. Melissa Haendel

Assistant Professor
Ontology Development Group, OHSU Library
www.ohsu.edu/library/ontology<http://www.ohsu.edu/library/ontology>
Department of Medical Informatics and Epidemiology
Oregon Health & Science University
haendel@ohsu.edu<mailto:haendel@ohsu.edu>
skype: melissa.haendel
503-407-5970
Received on Monday, 4 August 2014 16:57:04 UTC

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