Fwd: Decision on your PeerJ submission: "Achieving human and machine accessibility of cited data in scholarly publications" (#2014:12:3509:2:0:REVIEW)

[Tim Clark]

Manuscript accepted.

Begin forwarded message:

From: PeerJ <peer....@peerj.com>

Subject: Decision on your PeerJ submission: "Achieving human and machine accessibility of cited data in scholarly publications" (#2014:12:3509:2:0:REVIEW)

Reply-To: PeerJ <peer....@peerj.com>

To: Tim Clark <tim_...@harvard.edu>

Date: February 4, 2015 at 11:14:13 PM EST

PeerJ

Thank you for your submission to PeerJ. I am writing to inform you that your manuscript, "Achieving human and machine accessibility of cited data in scholarly publications" (#2014:12:3509:2:0:REVIEW), has been accepted for publication. My comments are as follows: Editor's comments Thanks for being open to the reviewer and editorial comments. If we need to clarify any details required to move the manuscript forward, then our production staff will get in touch with you. Otherwise, a proof will be forthcoming shortly for your review. Congratulations and thank you for your submission. Harry Hochheiser Academic Editor for PeerJ

© 2014, PeerJ, Inc. PO Box 614 Corte Madera, CA 94976, USA

[Ivan Herman]

Yay!

How does that work with PeerJ? I mean, I guess they have to 'officially' publish it; when does it happen and how?

Thanks Tim!

Ivan

>> © 2014, PeerJ, Inc. PO Box 614 Corte Madera, CA 94976, USA
>
>

> To unsubscribe from this group and stop receiving emails from it, send an email to idmeta+un...@force11.org.


----
Ivan Herman, W3C
Digital Publishing Activity Lead
Home: http://www.w3.org/People/Ivan/
mobile: +31-641044153
ORCID ID: http://orcid.org/0000-0003-0782-2704

[Stefan Proell]

Thanks Tim!

>> © 2014, PeerJ, Inc. PO Box 614 Corte Madera, CA 94976, USA
>

[Joan Starr]

Thanks Tim and congratulations to all!
--Joan

[Tim Clark]

I have just had a query from Peter Binfield - Publisher of PeerJ - whether we would rather this article appear in the inaugural issue of PeerJ Computer Science.  

Thoughts?

Tim

[Mercè Crosas]

I like the idea of publsihing in the first PeerJ computer Science

Mercè Crosas, Ph.D.

Director of Data Science, IQSS

Harvard University

http://datascience.iq.harvard.edu

[Ivan Herman]

> On 05 Feb 2015, at 14:13 , Tim Clark <tim_...@harvard.edu> wrote:
>
> I have just had a query from Peter Binfield - Publisher of PeerJ - whether we would rather this article appear in the inaugural issue of PeerJ Computer Science.
>
> Thoughts?

I actually think this would be a good idea. The paper is very much independent of various scholarly disciplines (medical, physics, etc.) and is more about usage of good computer science principles to be used in those areas.

Thanks

Ivan

[Robert R Downs]

I agree that it would be great to publish the paper in the inaugural issue of PeerJ. Congratulations Tim and all!

Thanks,

Bob

Robert R. Downs, PhD
Senior Digital Archivist and Senior Staff Associate Officer of Research
Center for International Earth Science Information Network (CIESIN),
The Earth Institute, Columbia University
P.O. Box 1000, 61 Route 9W, Palisades, NY 10964 USA
Voice: 845-365-8985; fax: 845-365-8922
E-mail:rdo...@ciesin.columbia.edu
Columbia University CIESIN Web site:http://www.ciesin.columbia.edu

[Robert R Downs]

PeerJ Computer Science!

[Joan Starr]

Nice idea! I do like the thematic fit and the extra splash. Did Pete say when it's scheduled to come out?
--Joan

[Ruth Ellen Duerr]

PeerJ Computer Science sounds good to me! - Ruth

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

"Those who would give up essential liberty to purchase a little temporary safety deserve neither liberty nor safety."

Benjamin Franklin, Historical Review of Pennsylvania, 1759

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Ruth Duerr

Data Stewardship and Informatics Lead

National Snow and Ice Data Center

Cooperative Institute for Research in Environmental Science

University of Colorado at Boulder

Boulder, CO 80309

(303) 735-0136

rdu...@nsidc.org

[Melissa Haendel]

me too!

On Feb 5, 2015, at 8:39 AM, Ruth Ellen Duerr <rdu...@Colorado.EDU>

 wrote:

Dr. Melissa Haendel

Associate Professor
Ontology Development Group, OHSU Library

www.ohsu.edu/library/ontology

Department of Medical Informatics and Epidemiology
Oregon Health & Science University
hae...@ohsu.edu
skype: melissa.haendel

503-407-5970

[Michel Dumontier]

+1

[Castro, Eleni]

Sounds like a good idea!

-- 

Eleni Castro
Research Coordinator, Data Acquisition and Archiving, Data Science
IQSS, Harvard University
http://www.iq.harvard.edu/people/eleni-castro 

We're redesigning Dataverse and want your feedback! Please check out our Beta Site.

[Simone Sacchi]

+1 on PeerJ Computer Science

–––––––––––––
Simone Sacchi
Research and Scholarship Initiatives Manager
CDRS – Center for Digital Research and Scholarship
Columbia University
http://www.cdrs.columbia.edu
Email: ssa...@columbia.edu — Phone: (212) 851-7339
Twitter: @simosacchi @ScholarlyComm
ORCID: 0000-0002-6635-7059

[Melissa Haendel]

almost immediately in my one experience :-)

[Ivan Herman]

Search on PeerJ leads only to

https://peerj.com/preprints/697/

ie, it is still the preprint.

But this is probably o.k., because we agreed that the article will be part of the inaugural issue of PeerJ Computer Science. I just wonder we know when PeerJ CS will really start...

Ivan

[Tim Clark]

I'll ask them. 

[Joan Starr]

Somewhere I have an email from you, Tim, that says CS starts in April.
--Joan

---

From: Tim Clark [tim_...@harvard.edu]
Sent: Saturday, February 28, 2015 6:22 AM
To: Dr Ivan Herman
Cc: Melissa Haendel; <idm...@force11.org>
Subject: Re: [idmeta] Decision on your PeerJ submission: "Achieving human and machine accessibility of cited data in scholarly publications" (#2014:12:3509:2:0:REVIEW)

[Melissa Haendel]

Some comments from a colleague on the preprint to consider:

From: Julie McMurry <jmcm...@ebi.ac.uk>

Subject: Substitute sentence for PeerJ paper

Date: March 12, 2015 3:39:45 PM PDT

To: Melissa Haendel <hae...@ohsu.edu>

Hi Melissa,

I recommend replacing the following sentence:

"For example, the DOI resolver at http://doi.org  resolves the DOI 10.1098/rsos.140216 to the URI http://rsos.royalsocietypublishing.org/content/1/3/140216.
And the identifiers.org resolution service, at http://identifiers.org, resolves the PubMed identifier 16333295 to http://www.ncbi.nlm.nih.gov/pubmed/16333295.” 

…with...

"For example, the DOI 10.1098/rsos.140216 when appended to the DOI resolver at http://doi.org, resolves to the URI http://rsos.royalsocietypublishing.org/content/1/3/140216.
“Similarly, the biosample identifier SAMEG120702, when appended as ("biosample/SAMEG120702") to the identifiers.org resolver at http://identifiers.org, resolves to the landing page www.ebi.ac.uk/biosamples/group/SAMEG120702.” 

Also, the following sentence....

"Landing pages should combine human-readable and machine-readable information on a selection of the following items.”
It seems like the content was reorganised such that what follows no longer makes sense.

Is it OK if the identifiers.org folks have a look at the proofs?

[Joan Starr]

Thanks Melissa.

She's right that this phrase: "Landing pages should combine human-readable and machine-readable information on a selection of the following items." can simply be deleted. I'm not a laTeX-fluent person so I'm going to have to leave fixing that to others.

As for getting more feedback from identifiers.org people (or anyone else)--why not? Maybe I'm missing something...

Joan 

---

From: Melissa Haendel [hae...@ohsu.edu]
Sent: Friday, March 13, 2015 6:58 PM
To: Joan Starr
Cc: Tim Clark; Dr Ivan Herman; <idm...@force11.org>

[Melissa Haendel]

Thanks Joan, I agree on both accounts.

On Mar 14, 2015, at 7:52 AM, Joan Starr <Joan....@ucop.edu>

 wrote:

Thanks Melissa.

She's right that this phrase: "Landing pages should combine human-readable and machine-readable information on a selection of the following items." can simply be deleted. I'm not a laTeX-fluent person so I'm going to have to leave fixing that to others.

As for getting more feedback from identifiers.org people (or anyone else)--why not? Maybe I'm missing something...

Joan 

---

From: Melissa Haendel [hae...@ohsu.edu]
Sent: Friday, March 13, 2015 6:58 PM
To: Joan Starr
Cc: Tim Clark; Dr Ivan Herman; <idm...@force11.org>
Subject: Re: [idmeta] Decision on your PeerJ submission: "Achieving human and machine accessibility of cited data in scholarly publications" (#2014:12:3509:2:0:REVIEW)

Some comments from a colleague on the preprint to consider:

From: Julie McMurry <jmcm...@ebi.ac.uk>

Subject: Substitute sentence for PeerJ paper

Date: March 12, 2015 3:39:45 PM PDT

To: Melissa Haendel <hae...@ohsu.edu>

Hi Melissa,

I recommend replacing the following sentence:

"For example, the DOI resolver at http://doi.org  resolves the DOI 10.1098/rsos.140216 to the URIhttp://rsos.royalsocietypublishing.org/content/1/3/140216.
And the identifiers.org resolution service, at http://identifiers.org, resolves the PubMed identifier 16333295 tohttp://www.ncbi.nlm.nih.gov/pubmed/16333295.” 

…with...

"For example, the DOI 10.1098/rsos.140216 when appended to the DOI resolver at http://doi.org, resolves to the URIhttp://rsos.royalsocietypublishing.org/content/1/3/140216.

[Tim Clark]

I'll contact PeerJ about making these changes.

[Melissa Haendel]

Thanks Tim!

On Mar 14, 2015, at 10:03 AM, Tim Clark <tim_...@harvard.edu>

 wrote:

[Tim Clark]

Let me ask a question about the title, since we are considering other potential edits to the article now   

Do we still think the title is an accurate description of the contents?  I.e., are we only talking about “accessibility”, which implies only read access, or do we really mean “actionability”, which includes read, write, update, delete, compute, etc. ?  

I suggest that a better and more descriptive title might be

“Achieving Machine Actionability of Cited Data in Scholarly Publications”. 

What do people think?

Tim

On Mar 14, 2015, at 11:20 AM, Melissa Haendel <hae...@ohsu.edu> wrote:

[Tim Clark]

Very cogently expressed, Joe. I can see you have thought about this issue.

Other thoughts from co-authors?



> On Mar 14, 2015, at 7:43 PM, one...@dcr.net wrote:

>
> Quoting Tim Clark <tim_...@harvard.edu>:
>
>> Let me ask a question about the title, since we are considering other potential edits to the article now
>>

>> Do we still think the title is an accurate description of the contents? I.e., are we only talking about ?accessibility?, which implies only read access, or do we really mean ?actionability?, which includes read, write, update, delete, compute, etc. ?

>>
>> I suggest that a better and more descriptive title might be
>>

>> ?Achieving Machine Actionability of Cited Data in Scholarly Publications?.

>>
>> What do people think?
>>
>> Tim
>

> (To summarize : I'm very much against the proposed title)
>
>
> I think that 'Actionability' requires understanding the data to be used, and the scientific data that I deal with doesn't have sufficient machine-readable documentation to be used by machines that had never encountered it.
>
> I believe that going from 'Accessible' to 'Actionable' is a step that we have even begun to discuss in this paper.
>
> I had a poster at the AAS meeting last year on the topic just concerning one scientific file format (FITS) :
>
> http://dx.doi.org/10.5281/zenodo.10226
>
> I would estimate that we're *at* *least* 5 years off from being able to create he necessary documentation for reliable machine actionability of FITS files, to describe what's in the files and the appropriate use caveats in a machine-understandable way. And that only handles *one* of the formats that we use; a significant amount of higher-level data products are still distributed as ASCII tables, HTML tables, IDL save files, Excel spteadsheets or tables embeded in PDF documents.
>
> -Joe
>
> ps. I would claim that 'Actionable' is 'Usable' under Peter Morville's "Facets of User Experience" ( http://semanticstudios.com/user_experience_design/ ). The only facet that we've touched on other than 'Accessible' is 'Findable' and not as a significant thrust of the paper.
>
>
>

[Ruth Ellen Duerr]

I have to agree with Joe. - Ruth

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

"Those who would give up essential liberty to purchase a little temporary safety deserve neither liberty nor safety."

Benjamin Franklin, Historical Review of Pennsylvania, 1759

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Ruth Duerr
Data Stewardship and Informatics Lead
National Snow and Ice Data Center
Cooperative Institute for Research in Environmental Science
University of Colorado at Boulder
Boulder, CO 80309
(303) 735-0136
rdu...@nsidc.org

[Joan Starr]

Joe and Ruth have much more refined definitions/understandings of these terms than I have been familiar with, so I defer to them.
--Joan

[Tim Clark]

OK, I surrender  :-)

No changes to title. 

Will contact the PeerJ folks about other edits discussed. 

[Mercè Crosas]

Even though I like the new title, with "machine actionable",  after thinking more about it, I do agree that based on the focus of this paper,  the term "machine accessible" is more accurate. 

Joe, let me add, however, that even though we haven't discussed the "actionable" part in this paper, the landscape for actionable data is not completly gloomy. For more than 5 years, we've been enabling to publish machine actionable tabular data in Dataverse  (in R Data, SPSS, Stata format; and more formats coming in 4.0, including the first steps for machine actionable FITS). Using metadata standards that the social science (ICPSR, ODUM and other archives) have been using for years, such as the DDI schema, we can document the column level (variable level) metadata in great detail, and enable other applications to explore, analyze, merge (in a few cases), and visualize (for example, maps, for geospatial data) the datasets published in such repositories through APIs. I agree, again, that this paper didn't focus on that - but you just made me think that I should write another paper on the work we've done for Dataverse 4.0 to describe these steps towards machine actionable tabular data, :) want to join?

Best,

Merce

Mercè Crosas, Ph.D.

Director of Data Science, IQSS

Harvard University

http://datascience.iq.harvard.edu