Other options for nexml_publish()

[sckott]

Seems that figshare is the only option right now. Correct @cboettig ?

• Perhaps we can include a options for github, either to repo, gist, or both?
• I imagine Dryad doesn't accept submissions programmatically?

Are there other places folks may want to share nexml files?

[cboettig]

Yup, that's correct. I'd like to add KNB so that it would part of the DataONE inventory. From what I understand DataONE has a NEXUS type but no NeXML type. Though maybe we could just use the XML type. See: https://cn.dataone.org/cn/v1/formats, @mbjones could probably set me straight on this.

Github is an interesting question. My intuition is not to, since for anyone using github already it's almost easier to do that without an R function, and for users not using github they might think "so where's my DOI?".

Dryad (& Treebase) are the most obvious targets for sure. IIRC @rvosa tells us that Treebase cannot accept NeXML at this time, and @hlapp tells us the Dryad doesn't (yet?) accept automatic submissions (or maybe the sword thing is up and running now?). I think it would certainly be a nice use case as we could fill out the Dryad metadata automatically and perhaps more thoroughly this way.

[sckott]

Right, I don't think Github is a great use case here, it makes sense for things like .geojson files that can be rendered as maps, e.g.

Yeah, i imagine since it's not free, Dryad would need users to authenticate somehow after payment is received?

[hlapp]

No, the SWORD interface is not up yet in Dryad.

[mbjones]

@cboettig That's right, at DataONE we have NEXUS registered as a format but not NeXML yet as far as I can see. We can easily add formats as needed, but like to set the format identifier to be that which is normally used by the community when typing their documents. Do you know what people use for the namespace identifier? Are there multiple versions with their own namespaces that correspond to different XSD versions? I read the paper on NexML, but the NeXML web site it refers to seems to be down, so I'd have to look around for the current home. I found a nexml github repo that had some example documents using a namespace of http://www.nexml.org/2009, so maybe that is the right namespace? If you can provide a list of namespace/names/versions for NeXML, I can help get them registered in the DataONE format list.

[rvosa]

There is only the one namespace that you mention: http://www.nexml.org/2009

Would it be helpful to know that NeXML is known to the EDAM ontology? Not
sure if that is at all useful but worth pointing out:
http://www.ebi.ac.uk/ontology-lookup/?termId=format%3A3160

On Fri, Aug 22, 2014 at 2:26 AM, Matt Jones notifications@github.com
wrote:

@cboettig https://github.com/cboettig That's right, at DataONE we have
NEXUS registered as a format but not NeXML yet as far as I can see. We can
easily add formats as needed, but like to set the format identifier to be
that which is normally used by the community when typing their documents.
Do you know what people use for the namespace identifier? Are there
multiple versions with their own namespaces that correspond to different
XSD versions? I read the paper on NexML
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376374/, but the NeXML web
site http://www.nexml.org/ it refers to seems to be down, so I'd have
to look around for the current home. I found a nexml github repo
https://github.com/nexml/nexml that had some example documents
https://github.com/nexml/nexml/blob/master/examples/phenoscape.xml
using a namespace of http://www.nexml.org/2009, so maybe that is the
right namespace? If you can provide a list of namespace/names/versions for
NeXML, I can help get them registered in the DataONE format list.

—
Reply to this email directly or view it on GitHub
#90 (comment).

[mbjones]

@cboettig @rvosa OK, I requested creation of the NeXML format by @csjx in DataONE issue 6068. Please comment on that ticket if anything looks awry with the proposed format info.

Should we differentiate the NEXUS/NeXML formats (http://www.nexml.org) from the similarly named NeXus/NeXML format in the neutron and xray community (http://www.nexusformat.org/)? Maybe its not an issue?

[rvosa]

@mbjones there is a definite possibility of confusion (I've seen it in a deeply embarrassing publication: http://www.deepdyve.com/lp/institute-of-electrical-and-electronics-engineers/the-design-of-ruby-rdf-api-for-evolutionary-informatics-fnVpOUe4Qs), hence it might make sense to also cite the EDAM term. Just FYI: the nexml.org domain will come back to life, I promise. I'm switching domain registrars.

[mbjones]

@rvosa Thanks for the info. Any chance I can get a copy of the XSD schema from somewhere before the nexml.org site comes back up?

[rvosa]

https://github.com/nexml/nexml/tree/master/xsd

On Fri, Aug 22, 2014 at 6:01 PM, Matt Jones notifications@github.com
wrote:

@rvosa https://github.com/rvosa Thanks for the info. Any chance I can
get a copy of the XSD schema from somewhere before the nexml.org site
comes back up?

—
Reply to this email directly or view it on GitHub
#90 (comment).

[hlapp]

@cboettig @rvosa OK, I requested creation of the NeXML format by @csjx in DataONE issue 6068. Please comment on that ticket if anything looks awry with the proposed format info.

Just as an FYI to everyone, DataONE issue 6068 has been implemented and closed (see the D1 registration record).

[cboettig]

Closing as NeXML is now a recognized type in DataONE. I think it would make sense that a user would upload to DataONE directly via the dataone package, I don't believe that the uploading process should really be in the scope of RNeXML.