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Re: GSoC 2018: Bioschemas application status

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Fri, 13 Apr 2018 13:35:39 +0100
To: Alice Allen <aallen@ascl.net>, Carl Boettiger <cboettig@gmail.com>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Martin Fenner <martin.fenner@datacite.org>, Paolo Manghi <paolo.manghi@isti.cnr.it>, Alessia Bardi <alessia.bardi@isti.cnr.it>, Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Cc: Helen Parkinson <parkinson@ebi.ac.uk>, Sirarat Sarntivijai <sirarat.sarntivijai@elixir-europe.org>, Stian Soiland-Reyes <soiland-reyes@manchester.ac.uk>, carole.goble@manchester.ac.uk
Message-ID: <443f80dd-1d6e-306a-7449-9e09d9505042@manchester.ac.uk>

Hi

I am also looping in Helen Parkinson and some other colleagues.

We discussed OpenAIRE and software metadata in the ELIXIR Interop call 
today and Helen has several suggestions of people to review the guidelines.

Carole



On 12/04/2018 11:18, Alice Allen wrote:
> Hi all, and thank you, Carole!
>
> The Astrophysics Source Code Library (ASCL, ascl.net 
> <http://ascl.net>) registers software (source code) used in astro 
> research (in peer-reviewed publications or close to that, such as PhD 
> theses); we generally point to the download site for the software we 
> register, but do upon author request house code ourselves. We have a 
> light metadata model for reasons explained in this paper 
> <https://openresearchsoftware.metajnl.com/articles/10.5334/jors.bv/>. 
> We are independent; we work with all astro publishers, not just the AAS.
>
> The public data for codes accepted to the ASCL can be downloaded in 
> json format here: http://ascl.net/code/json. Clicking in the data 
> window makes a few options show up (pretty print, save, copy).
>
> We recently were awarded funding to modify/expand our metadata a bit, 
> and also have a number of fields that we do not expose to the public, 
> some of which have to do with curation, and some of which we will 
> expose once we have populated them more fully.
>
> I’m on travel now and will look more closely at the shared information 
> linked to below when I am home. Thanks for looping me in; this all 
> looks very relevant!
>
> Best,
>
> Alice
> Editor, ASCL
>
>
> On Apr 12, 2018, at 11:10 AM, Carole Goble 
> <carole.goble@manchester.ac.uk <mailto:carole.goble@manchester.ac.uk>> 
> wrote:
>
>> 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!
>>>>>>>
>>>>>>>         	
>>>>>>>
>>>>>>>
>>>>>>>         	
>>>>>>>
>>>>>>>         This email was sent to A.J.G.Gray@hw.ac.uk
>>>>>>>         <mailto:A.J.G.Gray@hw.ac.uk>.
>>>>>>>
>>>>>>>         You are receiving this email because of your
>>>>>>>         participation in Google Summer of Code 2018.
>>>>>>>         https://summerofcode.withgoogle.com
>>>>>>>         <https://summerofcode.withgoogle.com/>
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>>>>>>>
>>>>>>>         	
>>>>>>>
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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 (seehttp://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 emailmelanie.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 <http://carlboettiger.info/>
>>>>>>
>>>>>
>>>>>     -- 
>>>>>     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 (seehttp://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 emailmelanie.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 <http://carlboettiger.info/>
>>>
>

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

tel: +44 161 275 6195
email: carole.goble@manchester.ac.uk
twitter: @CaroleAnneGoble
PA: Melanie Price <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.
If you haven't heard within a week you really should try again.
Received on Friday, 13 April 2018 12:36:10 UTC

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