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reml-generated EML should include metadata stating so #22
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@mbjones Is this a standard thing to do? Recommendation for how we encode it? |
I think the best place to add it is in /eml/dataset/methods/methodStep/software, and in the sibling description element describe the role that reml played in generating the metadata. You might also want to add the citation in that subtree to REML. EML is pretty flexible, so there are other options as well, but I think this is the most appropriate. |
Schema diagram is here: |
@mbjones Thanks, this makes sense. First two are done, but trying to wrap my head around EML I assume we cite software as I'm a bit confused why I don't see things like I see that the citation object is built around the endnote format. R's citation tools (and lots of other tools) can return citations in bibtex format; I'm wondering if there's anything clever that can be done here in place of just mapping each term by hand... |
@cboettig Yeah, software is probably best listed as Regarding why
which is a group inclusion. Follow the link to res:ResourceGroup and you'll see all of the fields. If you look at the diagram for eml-literature, you'll see that those fields in the group have been included by parsing the XSD (http://knb.ecoinformatics.org/software/eml/eml-2.1.1/eml-literature.png). |
Sounds good. Thanks for explaining the group inclusion with Yeah, Dryad uses the custom: I was hoping Shotton's group might be persuaded to make a xsd file for On Sun, Jul 7, 2013 at 4:45 PM, Matt Jones notifications@github.com wrote:
Carl Boettiger |
Definitely not trivial to extend -- many groups around the world use the EML schema and have written software to generate it and consume it -- any schema changes, especially backwards incompatible ones, have a ripple effect on the community. So, we try to avoid changes that break existing EML documents. Adding something as an optional new field is more acceptable and can generally get approved by the EML community fairly quickly. |
@mbjones Okay, I failed to write this My R code creates a nod that looks like this: <methods>
<methodsStep>
<software>
<license>CC0</license>
<version>0.0-1</version>
<implementation>
<distribution>
<online>
<url>https://github.com/ropensci/reml</url>
</online>
</distribution>
</implementation>
</software>
<description>An R package for reading, writing, integrating and publishing data
using the Ecological Metadata Language (EML) format.</description>
</methodsStep>
</methods> And the validator complains:
Um, does this mean I need |
What function generated that metadata? |
eml_write, which called eml_dataset, which calls
which uses eml_R_software creates that node... (using eml_software) On Sat, Jul 20, 2013 at 8:56 AM, Karthik Ram notifications@github.comwrote:
Carl Boettiger |
@cboettig -- Just pushed a fix -- "methodsStep" should have been "methodStep". |
thanks! On Sat, Jul 20, 2013 at 9:19 AM, Matt Jones notifications@github.comwrote:
Carl Boettiger |
oh, validator still unhappy:
|
What does the methodStep snippet look like now? The error message is just relating the schema rules, which are somewhat easier to grok in this image: http://knb.ecoinformatics.org/software/eml/eml-2.1.1/eml-methods.png |
now it is: <methods>
<methodStep>
<software>
<license>CC0</license>
<version>0.0-1</version>
<implementation>
<distribution>
<online>
<url>https://github.com/ropensci/reml</url>
</online>
</distribution>
</implementation>
</software>
<description>An R package for reading, writing, integrating and publishing data
using the Ecological Metadata Language (EML) format.</description>
</methodStep>
</methods> |
Elements need to be in a different order to be valid. In addition, you are missing required fields from the software module, including title, and creator. See: Something like this might validate (I didn't try it, just tried to follow the schema): <methods>
<methodStep>
<description>An R package for reading, writing, integrating and publishing data
using the Ecological Metadata Language (EML) format.</description>
<software>
<title>reml</title>
<creator>
<individualName>
<givenName>Carl</givenName><surName>Boettiger</surName>
</individualName>
</creator>
<creator>
<individualName>
<givenName>Karthik</givenName><surName>Ram</surName>
</individualName>
</creator>
<implementation>
<distribution>
<online>
<url>https://github.com/ropensci/reml</url>
</online>
</distribution>
</implementation>
<license>CC0</license>
<version>0.0-1</version>
</software>
</methodStep>
</methods> |
Thanks for clarifying, sorry I haven't got the hang of reading the spec still. I keep forgetting |
I don't have a complete understanding of the spec either. @mbjones can you suggest some readings that will allow me to get up to speed? |
@karthikram The pngs are pretty handy once you get the hang of them, e.g. Otherwise I find the descriptions in the 'normative technical documents' As I commented above, a working XMLSchema will be a big help in automating On Sat, Jul 20, 2013 at 9:23 PM, Karthik Ram notifications@github.comwrote:
Carl Boettiger |
The diagrams are the best way to understand the spec, although note that the diagrams do not show XML attributes. This was a shortcoming of the software used to generate the schemas. There is a nice explanation of the diagrams here: http://www.diversitycampus.net/projects/tdwg-sdd/minutes/SchemaDocu/SchemaDesignElements.html I'm not sure what you are referring to with the 'symbols with boxes on lines' comment. Sorry. Getting up to speed on the EML spec (or any other) just takes time -- the EML schema itself is the most useful. We wrote a paper describing use of the spec a while ago targeted at ecologists, but it doesn't get into the technical details of the spec -- see Fegraus et al. 2005: http://www.mendeley.com/download/public/1825821/4445891665/2d411d3da6a51fecf34b4f0061a68d250c486eaa/dl.pdf These diagrams were built with XML Spy, an XML editor that can display XML Schema. There are several others that will produce diagrams. If you are trying to understand the EML schema, it can be useful to open the eml.xsd schema in one of these editors so that you can explore the schema tree more dynamically -- the images are just static screenshots of the diagrams for certain subtrees. |
reml-generated methods node now exists, so I think we can close this issue. |
That way if someone doesn't like the EML, they know who to blame ;-)
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