include author information

egonw commented 7 years ago

Which is needed downstream for nanopublications, but actually for any system that uses the citation expectations for WikiPathways outlined at http://www.wikipathways.org/index.php/How_to_cite_WikiPathways

DeniseSl22 commented 6 years ago

But this is not stored in the GPML, since it is only registered on the Website, right?

egonw commented 6 years ago

Correct.

AlexanderPico commented 4 years ago

This may or may not be helpful, but here is how I've extracted relevant author information per pathway directly from the database:

SELECT page_title AS WPID, rev_user AS userID, user_name AS userName, user_real_name AS realName, COUNT(rev_user) AS editCount, MIN(rev_timestamp) AS firstEdit 
FROM revision LEFT JOIN page ON revision.rev_page = page.page_id 
LEFT JOIN user ON revision.rev_user = user.user_id 
WHERE page_namespace = 102 AND page_title LIKE 'WP%' 
GROUP BY page_title, rev_user;

For RDF purposes, however, it may be more prudent to wait for the author information to be added to the GPML and then pull it from there.

AlexanderPico commented 4 years ago

Here are prototype ttl files with author strings and as wikidata entries (where available):

egonw commented 4 years ago

Ah, thanks for starting this. Some comments:

let's use a machine readable model (then easier to add ORCID and other info)
the URI of the pathway needs to include the revision of the RDF export (that will be a challenge)

Suggestion:

@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml:  <http://vocabularies.wikipathways.org/gpml#> .
@prefix dc:    <http://purl.org/dc/elements/1.1/>
@prefix foaf:  <http://xmlns.com/foaf/0.1/>

<http://identifiers.org/wikipathways/WP1_r107192>
        dc:creator            <http://rdf.wikipathways.org/User/Nsalomonis> .

<http://rdf.wikipathways.org/User/Nsalomonis>
        a             foaf:Person ;
        foaf:name     "Nathan Salomonis" ;
        foaf:homepage <https://www.wikipathways.org/index.php/User:Nsalomonis> .

And similarly for the ORCID part, I propose:

<http://rdf.wikipathways.org/User/AlexanderPico>
        owl:sameAs    <https://www.wikidata.org/wiki/Q28530149> ;
        foaf:name     "Alexander R. Pico" ;
        dc:identifier <https://orcid.org/0000-0001-5706-2163> .

AlexanderPico commented 4 years ago

Right. When this gets added to the wp ttl files, the pathway revision informaiton will already be in hand (as it is currenlty). I can update the rest of the data in the prototype files to follow your proposal.

Question: should we not use gpml:author anywhere? Perhaps it's just not needed given the dc and foaf definitions already in use?

AlexanderPico commented 4 years ago

@egonw, @ariutta Changes made per your suggestions, combining all info into a single file per pathway. See new zip of ttls at http://data.wikipathways.org/20190910/rdf/wikipathways-20190910-rdf-authors.zip and a sample here:

@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix gpml:  <http://vocabularies.wikipathways.org/gpml#> .
@prefix dc:    <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#>.
@prefix foaf:  <http://xmlns.com/foaf/0.1/> .

<http://identifiers.org/wikipathways/WP100>
        dc:creator            <http://rdf.wikipathways.org/User/Andra> , <http://rdf.wikipathways.org/User/Thomas> , <http://rdf.wikipathways.org/User/AlexanderPico> , <http://rdf.wikipathways.org/User/Khanspers> , <http://rdf.wikipathways.org/User/Egonw> , <http://rdf.wikipathways.org/User/DeSl> .

<http://rdf.wikipathways.org/User/Andra>
        a                    foaf:Person ;
        foaf:name            "Andra Waagmeester ;
        owl:sameAs           <https://www.wikidata.org/wiki/Q19845625> ;
        dc:identifier        <https://orcid.org/0000-0001-9773-4008> ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:Andra> .

<http://rdf.wikipathways.org/User/Thomas>
        a                    foaf:Person ;
        foaf:name            "Thomas Kelder ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:Thomas> .

<http://rdf.wikipathways.org/User/AlexanderPico>
        a                    foaf:Person ;
        foaf:name            "Alexander Pico ;
        owl:sameAs           <https://www.wikidata.org/wiki/Q28530149> ;
        dc:identifier        <https://orcid.org/0000-0001-5706-2163> ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:AlexanderPico> .

<http://rdf.wikipathways.org/User/Khanspers>
        a                    foaf:Person ;
        foaf:name            "Kristina Hanspers ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:Khanspers> .

<http://rdf.wikipathways.org/User/Egonw>
        a                    foaf:Person ;
        foaf:name            "Egon Willighagen ;
        owl:sameAs           <https://www.wikidata.org/wiki/Q20895241> ;
        dc:identifier        <https://orcid.org/0000-0001-7542-0286> ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:Egonw> .

<http://rdf.wikipathways.org/User/DeSl>
        a                    foaf:Person ;
        foaf:name            "Denise Slenter ;
        owl:sameAs           <https://www.wikidata.org/wiki/Q43744369> ;
        dc:identifier        <https://orcid.org/0000-0001-8449-1318> ;
        foaf:homepage        <https://www.wikipathways.org/index.php/User:DeSl> .

egonw commented 4 years ago

Nice! I do spot a missing quote at the end of the name:

foaf:name            "Andra Waagmeester ;

AlexanderPico commented 4 years ago

Good catch! Fixed and reupladed to http://data.wikipathways.org/20190910/rdf/wikipathways-20190910-rdf-authors.zip

wikipathways / GPML2RDF

include author information #33