I'm at the Crossref LIVE 16 event in London where I just gave a

on WikiCite and Wikidata targeted at scholarly publishers. Beside Crossref and Datacite people, I talked to a bunch of folks

in collaborating on Wikidata integration, particularly from PLOS, Hindawi and Springer Nature. I started an interesting discussion with Andrew

who runs strategic projects at Hindawi, and I wanted to open it up to everyone on the lists. Andrew asked me if – aside from efforts like ContentMine and StrepHit – there are any recommendations for publishers (especially OA publishers)

mark up their contents and facilitate information extraction and entity matching or even push triples to Wikidata to be considered for ingestion. I don't think we have a recommended workflow for data providers for facilitating triple suggestions to Wikidata, other than leveraging the Primary Sources Tool. However, aligning keywords and terms with the corresponding Wikidata items via ID mapping sounds like a good first

pointed Andrew to Mix'n'Match as a handy way of mapping identifiers, but

you have other ideas on how to best support 2-way integration of Wikidata with scholarly contents, please chime in. Dario -- Dario Taraborelli Head of Research, Wikimedia Foundation wikimediafoundation.org • nitens.org • @readermeter -- WikiCite 2016 – May 26-26, 2016, Berlin Meta: https://meta.wikimedia.org/wiki/WikiCite_2016 Twitter: https://twitter.com/wikicite16 --- You received this message because you are subscribed to the Google Groups "wikicite-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to wikicite-discuss+unsubscribe(a)wikimedia.org.

Dario, One message you can send is that they can and should use existing controlled vocabularies and ontologies to construct the metadata they want to share. For example, MeSH descriptors would be a good way for them to organize the 'primary topic' assertions for their articles and would make it easy to find the corresponding items in Wikidata when uploading. Our group will be continuing to expand coverage of identifiers and concepts from vocabularies like that in Wikidata - and any help there from publishers would be appreciated! My view here is that Wikidata can be a bridge to the terminologies and datasets that live outside it - not really a replacement for them. So, if they have good practices about using shared vocabularies already, it should (eventually) be relatively easy to move relevant assertions into the WIkidata graph while maintaining interoperability and integration with external software systems. -Ben On Wed, Nov 2, 2016 at 8:31 AM, 'Daniel Mietchen' via wikicite-discuss < wikicite-discuss(a)wikimedia.org&gt; wrote:

Regarding the topics/vocabularies issue: A challenge we're working on is finding a set of controlled vocabularies for all the subject areas we cover. We do use MeSH for those subjects, but this only applies to about 40% of our papers. In Engineering, for example, we've had more trouble finding an open taxonomy with the same level of depth as MeSH. For most internal applications, we need 100% coverage of all subjects. Machine learning for concept tagging is trendy now, partly because it doesn't require a preset vocabulary, but we are somewhat against this approach because we want to control the mapping of terms and a taxonomic hierarchy can be useful. The current ML tools I've seen can match to a controlled vocabulary, but then they need the publisher to supply the terms. The temptation to build a new vocabulary is strong, because it's the fastest way to get to something that is non-proprietary and universal. We can merge existing open vocabularies like MeSH and PLOS to get most of the way there, but we then need to extend that with concepts from our corpus. Thanks Daniel and Benjamin for your responses. Any other feedback would be great, and I'm always happy to delve into issues from the publisher perspective if that can be helpful. On Fri, Nov 11, 2016 at 4:54 PM, Dario Taraborelli < dtaraborelli(a)wikimedia.org&gt; wrote: Benjamin – agreed, I too see Wikidata as mainly a place to hold all the mappings. Once we support federated queries in WDQS, the benefit of ID mapping (over extensive data ingestion) will become even more apparent. Hope Andrew and other interested parties can pick up this thread. On Wed, Nov 2, 2016 at 12:11 PM, Benjamin Good &lt;ben.mcgee.good(a)gmail.com&gt; wrote: Dario, One message you can send is that they can and should use existing controlled vocabularies and ontologies to construct the metadata they want to share. For example, MeSH descriptors would be a good way for them to organize the 'primary topic' assertions for their articles and would make it easy to find the corresponding items in Wikidata when uploading. Our group will be continuing to expand coverage of identifiers and concepts from vocabularies like that in Wikidata - and any help there from publishers would be appreciated! My view here is that Wikidata can be a bridge to the terminologies and datasets that live outside it - not really a replacement for them. So, if they have good practices about using shared vocabularies already, it should (eventually) be relatively easy to move relevant assertions into the WIkidata graph while maintaining interoperability and integration with external software systems. -Ben On Wed, Nov 2, 2016 at 8:31 AM, 'Daniel Mietchen' via wikicite-discuss < wikicite-discuss(a)wikimedia.org&gt; wrote: I'm traveling ( https://twitter.com/EvoMRI/status/793736211009536000 ), so just in brief: In terms of markup, some general comments are in https://www.ncbi.nlm.nih.gov/books/NBK159964/ , which is not specific to Hindawi but partly applies to them too. A problem specific to Hindawi (cf. https://commons.wikimedia.org/wiki/Category:Media_from_Hindawi) is the bundling of the descriptions of all supplementary files, which translates into uploads like https://commons.wikimedia.org/wiki/File:Evolution-of-Coronary-Flow-in-an- Experimental-Slow-Flow-Model-in-Swines-Angiographic-and-623986.f1.ogv (with descriptions for nine files) and eight files with no description, e.g. https://commons.wikimedia.org/wiki/File:Evolution-of-Coronary-Flow-in-an- Experimental-Slow-Flow-Model-in-Swines-Angiographic-and-623986.f2.ogv . There are other problems in their JATS, and it would be good if they would participate in http://jats4r.org/ . Happy to dig deeper with Andrew or whoever is interested. Where they are ahead of the curve is licensing information, so they could help us set up workflows to get that info into Wikidata. In terms of triple suggestions to Wikidata: - as long as article metadata is concerned, I would prefer to concentrate on integrating our workflows with the major repositories of metadata, to which publishers are already posting. They could help us by using more identifiers (e.g. for authors, affiliations, funders etc.), potentially even from Wikidata (e.g. for keywords/ P921, for both journals and articles) and by contributing to the development of tools (e.g. a bot that goes through the CrossRef database every day and creates Wikidata items for newly published papers). - if they have ways to extract statements from their publication corpus, it would be good if they would let us/ ContentMine/ StrepHit etc. know, so we could discuss how to move this forward. d. On Wed, Nov 2, 2016 at 1:42 PM, Dario Taraborelli &lt;dtaraborelli(a)wikimedia.org&gt; wrote: presentation interested Hindawi Smeall, to ingestion. step. I but if Wikidata Groups an -- WikiCite 2016 – May 26-26, 2016, Berlin Meta: https://meta.wikimedia.org/wiki/WikiCite_2016 Twitter: https://twitter.com/wikicite16 --- You received this message because you are subscribed to the Google Groups "wikicite-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to wikicite-discuss+unsubscribe(a)wikimedia.org. -- *Dario Taraborelli *Head of Research, Wikimedia Foundation wikimediafoundation.org • nitens.org • @readermeter <http://twitter.com/readermeter> -- WikiCite 2016 – May 26-26, 2016, Berlin Meta: https://meta.wikimedia.org/wiki/WikiCite_2016 Twitter: https://twitter.com/wikicite16 --- You received this message because you are subscribed to the Google Groups "wikicite-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to wikicite-discuss+unsubscribe(a)wikimedia.org. -- ------------------------------ Andrew Smeall Head of Strategic Projects Hindawi Publishing Corporation Kirkman House 12-14 Whitfield Street, 3rd Floor London, W1T 2RF United Kingdom ------------------------------ _______________________________________________ Wikidata mailing list Wikidata(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata

Regarding the topics/vocabularies issue: A challenge we're working on is finding a set of controlled vocabularies for all the subject areas we cover. We do use MeSH for those subjects, but this only applies to about 40% of our papers. In Engineering, for example, we've had more trouble finding an open taxonomy with the same level of depth as MeSH. For most internal applications, we need 100% coverage of all subjects. Machine learning for concept tagging is trendy now, partly because it doesn't require a preset vocabulary, but we are somewhat against this approach because we want to control the mapping of terms and a taxonomic hierarchy can be useful. The current ML tools I've seen can match to a controlled vocabulary, but then they need the publisher to supply the terms. The temptation to build a new vocabulary is strong, because it's the fastest way to get to something that is non-proprietary and universal. We can merge existing open vocabularies like MeSH and PLOS to get most of the way there, but we then need to extend that with concepts from our corpus. Thanks Daniel and Benjamin for your responses. Any other feedback would be great, and I'm always happy to delve into issues from the publisher perspective if that can be helpful. On Fri, Nov 11, 2016 at 4:54 PM, Dario Taraborelli < dtaraborelli(a)wikimedia.org&gt; wrote: -- ------------------------------ Andrew Smeall Head of Strategic Projects Hindawi Publishing Corporation Kirkman House 12-14 Whitfield Street, 3rd Floor London, W1T 2RF United Kingdom ------------------------------ -- WikiCite 2016 – May 26-26, 2016, Berlin Meta: https://meta.wikimedia.org/wiki/WikiCite_2016 Twitter: https://twitter.com/wikicite16 --- You received this message because you are subscribed to the Google Groups "wikicite-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to wikicite-discuss+unsubscribe(a)wikimedia.org.

We do use MeSH for those subjects, but this only applies to about 40% of our papers. In Engineering, for example, we've had more trouble finding

open taxonomy with the same level of depth as MeSH.

For most internal applications, we need 100% coverage of all subjects.

The temptation to build a new vocabulary is strong, because it's the fastest way to get to something that is non-proprietary and universal. We can merge existing open vocabularies like MeSH and PLOS to get most of

way there, but we then need to extend that with concepts from our corpus.

Andrew Smeall writes an Have you found one? Meaning you want to have a scheme that provides at least one class for any of the papers that you publish? Why? We the corpus. I am not sure I follow this. Surely, if you don't have categories for engineering, you can build your own scheme and publish it. I don't see this as a reason for not using MESH when that is valid for the paper under consideration. I must be missing something. -- Cheers, Thomas Krichel http://openlib.org/home/krichel skype:thomaskrichel

Dario, One message you can send is that they can and should use existing controlled vocabularies and ontologies to construct the metadata they want to share. For example, MeSH descriptors would be a good way for them to organize the 'primary topic' assertions for their articles and would make it easy to find the corresponding items in Wikidata when uploading. Our group will be continuing to expand coverage of identifiers and concepts from vocabularies like that in Wikidata - and any help there from publishers would be appreciated! My view here is that Wikidata can be a bridge to the terminologies and datasets that live outside it - not really a replacement for them. So, if they have good practices about using shared vocabularies already, it should (eventually) be relatively easy to move relevant assertions into the WIkidata graph while maintaining interoperability and integration with external software systems. -Ben On Wed, Nov 2, 2016 at 8:31 AM, 'Daniel Mietchen' via wikicite-discuss < wikicite-discuss(a)wikimedia.org&gt; wrote:

Dario, I would love for the WDQS to support federated queries. Since we

Perhaps add a few to use as examples to start (uniprot and wikipathways would be good starters for our group). And then start an endpoint inclusion process accessible to the community through something akin to the property proposal pattern