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Re: hcls dataset description comments

From: Joachim Baran <joachim.baran@gmail.com>
Date: Thu, 31 Jul 2014 15:42:52 -0700
Message-ID: <CAObSwHX+o_PjdLn7GvPT+tx-1EwtsTVgSMsrmrTsEKgNKFWT6Q@mail.gmail.com>
To: Michael Miller <Michael.Miller@systemsbiology.org>
Cc: w3c semweb hcls <public-semweb-lifesci@w3.org>
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
>
>
>
>
>
>
>
>
>
Received on Thursday, 31 July 2014 22:43:20 UTC

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