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Re: GSoC 2018: Bioschemas application status

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Thu, 12 Apr 2018 09:10:08 +0000
To: Carl Boettiger <cboettig@gmail.com>, Alice Allen <aallen@ascl.net>
CC: Paolo Manghi <paolo.manghi@isti.cnr.it>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Alessia Bardi <alessia.bardi@isti.cnr.it>, "Miriam Baglioni" <miriam.baglioni@isti.cnr.it>, Martin Fenner <martin.fenner@datacite.org>, Carole Goble <carole.goble@manchester.ac.uk>
Message-ID: <B466A92E-D414-48E7-86B9-C1A73752F77E@manchester.ac.uk>
Hi all
Looping in Alice Allen ( curator of the Astro source code library for AAS) who can give a different perspective
Carole

Sent from my iPhone by
Professor Carole Goble
The University of Manchester
UK

On 10 Apr 2018, at 17:00, Carl Boettiger <cboettig@gmail.com<mailto:cboettig@gmail.com>> wrote:

Hi Paolo,

Thanks, these look great, will try and give this a run through when I'm looking at a larger screen.

I'm looping in Martin Fenner from DataCite since I think he's already done the mappings for DataCite to codemeta v2 / schema.org<http://schema.org>,
and may be able to weigh in here too.

Cheers,

Carl

On Tue, Apr 10, 2018 at 2:53 AM Paolo Manghi <paolo.manghi@isti.cnr.it<mailto:paolo.manghi@isti.cnr.it>> wrote:
Dear Carl and Carole,

Here we are again :) Since our last contact we had very useful interactions (and inputs) with DOE CODE (osti.gov<http://osti.gov>) and SSI in the UK. We would be therefore extremely glad to complete this picture with Codemeta.
We hope you can find the time to revise guidelines<http://software-guidelines.readthedocs.io/en/latest/index.html> and mappings<https://docs.google.com/spreadsheets/d/1mKs-Pg_JuLcpqEkQqlSCs2gGC7nEEbhxdTbIoGcU6NI/edit?usp=sharing> at the URLs below.

Let us know if there is anything we can do to support you.

Thank you in advance!

Paolo

----
Paolo Manghi
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR
Tel: +39 050 621-2038<tel:+39%20050%20621%202038> - Fax: +39 050 621-3464<tel:+39%20050%20621%203464>
Web page: http://nemis.isti.cnr.it/person/paolo-manghi
InfraScience Research Group: http://nemis.isti.cnr.it/groups/infrascience<http://laboratorio.isti.cnr.it/groups/infrascience>




On 20 Feb,2018, at 14:20 , Paolo Manghi <paolo.manghi@isti.cnr.it<mailto:paolo.manghi@isti.cnr.it>> wrote:

Dear Both,

Apologie for the delayed answer and many thanks for making this contact possible!

Carl, as OpenAIRE we are working on a light-weight metadata format, mainly inspired by DataCite, to describe software citation. We have started from DataCite and then looking at how other more software oriented initiatives were doing with respect to description for citation/reward properties. The main two being CodeMeta and SHARE-OMTD.

You can find a first draft of the guidelines here:

http://software-guidelines.readthedocs.io/en/latest/index.html

with

  *   introduction: http://software-guidelines.readthedocs.io/en/latest/introduction.html
  *   application profile: http://software-guidelines.readthedocs.io/en/latest/application_profile.html

You can find here the crosswalks from CodeMeta and OMTD here:

https://docs.google.com/spreadsheets/d/1mKs-Pg_JuLcpqEkQqlSCs2gGC7nEEbhxdTbIoGcU6NI/edit?usp=sharing

OpenAIRE is building a citation graph of research products: literature, datasets, software and “other products” (e.g. experiments, research objects, protocols, workflows). The idea is to leverage Open Science publishing principles, favour transparent evaluation and reproducibility, by opening up the “hidden part of science". Building this graph involves harvesting metadata from thousands of data sources and text mining millions of full-texts, to identify links between publications and datasets and software products (we collaborate with SoftwareHeritage):

  *   Harvest We mainly harvest software metadata from institutional publication repositories, where the are described using Dublin Core like standards and often bear a link to the relative software repository.
  *   Mining  When we perform mining and find a link to a software repository, as you know we can instead identify very poor metadata properties.

Given the context (software is either NOT described as a research product or, when it is, it is not managed as software should be), the idea was to identify a minimal set of mandatory properties required to describe a research software in OpenAIRE, targeting a pragmatic and citation-oriented approach. The main challenge was to decide which properties were in and out, keeping in mind our goal, a good dose of pragmatism given what is out there at the moment, and giving a glance to the future to push for better behaviour.

Best,

Paolo

----
Paolo Manghi
Istituto di Scienza e Tecnologie dell'Informazione "A. Faedo" - CNR
Tel: +39 050 621-2038<tel:+39%20050%20621%202038> - Fax: +39 050 621-3464<tel:+39%20050%20621%203464>
Web page: http://nemis.isti.cnr.it/person/paolo-manghi
InfraScience Research Group: http://nemis.isti.cnr.it/groups/infrascience<http://laboratorio.isti.cnr.it/groups/infrascience>




On 12 Feb,2018, at 19:18 , Carole Goble <carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk>> wrote:



Hi Carl!!

CodeMeta<https://codemeta.github.io/> was being namechecked by the openAIRE-Connect<https://www.openaire.eu/connect> project as the basis of their software scheme for openAIRE<https://www.openaire.eu/>.  They are also keen to link up with Bioschemas.

cheers

Carole


On 12/02/2018 18:12, Carl Boettiger wrote:
Hi All,

I'd second Carole's proposal (hi Carole!) and would love to see the proposed tasks.  (I've only just joined bioschemas so didn't see the GSOC proposal; though have enjoyed working with GSOC students on other work in years past).

I get a few dozen UC Berkeley undergrad CS students interested in independent research projects in this area each semester, way more than I have the capacity to work with.  I'd love to connect with potential mentors of the BioSchemas group to see if there are any those students who might want to work on those tasks. These students get only course credit rather than stipends for this, but I think would be interested in connecting to the broader bioschemas community as well.  Just a thought, at least  for fall 2018 semester if not before.

Cheers!

Carl

http://carlboettiger.info<http://carlboettiger.info/>

On Mon, Feb 12, 2018 at 10:03 AM Carole Goble <carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk>> wrote:


we could still post these as things we would like doning for folks to pick off
carole


On 12/02/2018 17:27, Gray, Alasdair J G wrote:
Thanks to everyone for their efforts in the Google summer of code proposal. Unfortunately it is bad news.

Alasdair

Alasdair J G Gray
Fellow of the Higher Education Academy
Assistant Professor in Computer Science
Heriot-Watt University, Edinburgh

www.macs.hw.ac.uk/~ajg33<http://%3Cbr/%3Ewww.macs.hw.ac.uk/%7Eajg33>

________________________________
From: Google Summer of Code <summerofcode-noreply@google.com><mailto:summerofcode-noreply@google.com>
Sent: Monday, February 12, 2018 5:06:08 PM
To: Gray, Alasdair J G
Subject: GSoC 2018: Bioschemas application status



[Google Summer of Code]

Thank you for applying to be a Google Summer of Code 2018 mentor organization. Sadly, we were unable to accept Bioschemas this year. We had many more applications than available slots. We hope you will apply again in the future!






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--
Professor Carole Goble CBE FREng FBCS CITP
School of Computer Science
University of Manchester
Manchester, UK

tel: +44 161 275 6195<tel:+44%20161%20275%206195>
email: carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk>
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--
Professor Carole Goble CBE FREng FBCS CITP
School of Computer Science
University of Manchester
Manchester, UK

tel: +44 161 275 6195<tel:+44%20161%20275%206195>
email: carole.goble@manchester.ac.uk<mailto:carole.goble@manchester.ac.uk>
twitter: @CaroleAnneGoble
PA: Melanie Price <melanie.j.price@manchester.ac.uk><mailto:melanie.j.price@manchester.ac.uk>

PLEASE NOTE: I no longer work weekends. You will not get a response.

email etiquette:
I get a lot of email and when I travel it gets even more backed up.

- Don't get too upset if my replies are short (see http://www.phdcomics.com/comics/archive.php?comicid=1047)
- If you don't get a reply within 48 hours there is a good chance the email has scrolled into the distance. If its urgent try again or email melanie.price@manchester.ac.uk<mailto:melanie.price@manchester.ac.uk>.
If you haven't heard within a week you really should try again.


--

http://carlboettiger.info
Received on Thursday, 12 April 2018 09:10:43 UTC

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