Melissa37
commented
6 years ago On further reading of the PubMed information online, we have clarified that this is the correct way to add data citations to our PubMed deliveries: My Question: Regarding submitting datasets, I am a bit confused by the documentation. Here an object type value of "Dataset" is provided, but here Dataset repository names are provided as the Dataset object type value.
Using the first example, I'd assume the tagging should be:
<Object Type="Dataset">
<Param Name="type">Dryad</Param>
<Param Name="id">10.5061/dryad.2f050</Param>
</Object>But for the second the tagging should be:
<Object Type="Dryad">
<Param Name="id">10.5061/dryad.2f050</Param>
</Object>
</ObjectList>PubMed response The first example that you cite from the help would be used to create a linking pair of citations. We commonly use this structure to link comments and corrections to their original article, and the other linking pairs have been grouped in the same category. If you had a PubMed citation to an article, and a second PubMed citation describing a dataset related to the original article, you could create a link between the two. The XML would look like:
<Object Type="dataset">
<Param Name="type">pmid</Param>
<Param Name="id">25264877</Param>
</Object>This would link the article citation to the dataset citation. (You could also make the link using the dataset ctiation’s DOI rather than the PMID.)
The second example is the XML that you would submit to create an external link to the dataset. …
<Object Type="Dryad">
<Param Name="id">10.5061/dryad.2f050</Param>
</Object>So, it seems we can only submit datasets from their list for Object, and just using the one example above, I have found a gap of proteomecentral.proteomexchange or PXD: Keyword Comment Dataset Erratum Originalreport Partialretraction Patientsummary Reprint Republished Retraction Update ANZCTR BioProject ClinicalTrials.gov CRiS CTRI ChiCTR DRKS Dryad EudraCT Figshare GDB IRCT ISRCTN JapicCTI JMACCT JPRN NTR Omim PACTR PDB PIR RPCEC ReBec SLCTR SwissProt TCTR UMINCTR UniMES UniParc UniProtKB UniRef NCBI:dbgap NCBI:dbvar NCBI:genbank NCBI:genome NCBI:gensat NCBI:geo NCBI:homologene NCBI:nucleotide NCBI:popset NCBI:protein NCBI:pubchem-bioassay NCBI:pubchem-compound NCBI:pubchem-substance NCBI:refseq NCBI:snp NCBI:sra NCBI:structure NCBI:taxonomy NCBI:unigene NCBI:unists
gnott
fred-atherden
In future, it would be good to take anything listed in the Major datasets generated section:
and convert, example:
However, in this section I don't think we are storing the information in a way it can be parsed for this data, WDYT @gnott ? This links t the work ongoing regarding Data Availability Statements.
Plan I have as at Feb 1, 2019:
assigning-authorityvalue from datasets in the article XML as a new value in the datasets JSON output namedassigningAuthoritydataIdvalues from thepub-idtag when appropriate (currently it only takes them fromobject-id"art-access-id"type tags)elife-articleDatasetobject, something likeassigning_authorityassigningAuthorityvalue to populateDatasetobjectsassigning_authorityvalue when parsing from XML to eLife article objectselife-pubmed-xml-generation, add<Object>tags for the datasets, including either the DOI value or accession id / dataId value, as is specified in the original article XML<Object><Param Name="type">value in the PubMed deposit for where the dataset is located