for instance, it should be easy to request a tree stored in treebase if the study is d

From <a href="https://github.com/OpenTreeOfLife/phylesystem-api/wiki/NexSON#table-i-pr

Hi <a class="user-mention notranslate" data-hovercard-type="user" data-hovercard-url="

Provide integration with other packages for study metadata about rotl HOT 5 CLOSED

ropensci commented on September 25, 2024

Provide integration with other packages for study metadata

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Comments (5)

dwinter commented on September 25, 2024

From this page it seems like ^ot:dataDeposit is always going to by a url (for dryad or treebase or whatever), so maybe

get_study_external_data <- function(sm){
   sm[["nexml"]][["^ot:dataDeposit"]][["@href"]]
}

Which works when there is a a link and returns NULL otherwise -- don't know if NA is better in this case? There is probably also a better function name

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dwinter commented on September 25, 2024

It occurs to me, having the DOIs make it straightforward to find nucleotide sequences if they exist in NCBI. Takes a bit of messing around with characters but something like this:

sm <- get_study_meta("pg_1940")
sm_doi <- sm[["nexml"]][["^ot:studyPublication"]][["@href"]]
doi_term = paste0(sub("http://dx.doi.org/", "", sm_doi), "[doi]")
paper <-  rentrez::entrez_search(db="pubmed", term=doi_term)
linked <- rentrez::entrez_link(dbfrom="pubmed", db="popset", id= paper$ids)
linked$links$pubmed_popset

[1] "295388201" "295388169" "295388107" "295388070" "295388035"

If we think this sort of thing is useful I'm happy to work integrating (at least) treebase, fulltext and rentrez into a get_external_data(ottid, data_source, ...) sort of function?

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fmichonneau commented on September 25, 2024

Hi @dwinter,

Yes, it would be great if you could started with this!

I like the idea of a get_external_data function.

There are a few methods to retrieve elements of the meta data associated with studies.

For instance, get_publication(get_study_meta("pg_1940")) will return the string about the publication and the DOI as an attribute:

[1] "Van der Linde, K., Houle D., Spicer G.S., & Steppan S. 2010. A supermatrix-based molecular phylogeny of the family Drosophilidae. Genetics Research 92 (1): 25-38."
attr(,"DOI")
[1] "http://dx.doi.org/10.1017/S001667231000008X"

I am currently working on improving the interface with the studies_find_studies and studies_find_trees functions to return more information than just the identifiers so users can look into the studies before selecting them. I'll request feedback when I think I have something that works (probably later today).

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dwinter commented on September 25, 2024

Have finally made a start on this. In case anyone has comments about the design here's what I have for now. A function to fin external IDs:

links <- study_external_IDs("pg_1940")
links

External data identifiers for study pg_1940 
 $doi:  10.1017/S001667231000008X 
 $pubmed_id:  20433773 
 $popset_ids: vector of 5 IDs 
 $nucleotide_ids: vector of 164 IDs
 $external_data_url http://purl.org/phylo/treebase/phylows/study/TB2:S10691

And a couple of functions to summarize the available data

summarize_nucleotide_data(links$nucleotide_ids[1:10])


                uid
295388256 295388256
295388254 295388254
295388253 295388253
295388251 295388251
295388249 295388249
295388247 295388247
295388245 295388245
295388243 295388243
295388241 295388241
295388239 295388239
                                                                                                                      title
295388256                Hirtodrosophila thoracis cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388254                 Hirtodrosophila duncani cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388253 Hirtodrosophila sp. KVDL-2010 cytochrome c oxidase subunit III-like (COIII) gene, partial sequence; mitochondrial
295388251                Mycodrosophila claytonae cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388249                     Drosophila pinicola cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388247                   Drosophila macrospina cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388245                    Drosophila guttifera cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388243                      Drosophila falleni cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388241                      Zaprionus indianus cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
295388239                     Zaprionus sepsoides cytochrome c oxidase subunit III (COIII) gene, partial cds; mitochondrial
          slen                      organism completeness
295388256  445      Hirtodrosophila thoracis             
295388254  445       Hirtodrosophila duncani             
295388253  363 Hirtodrosophila sp. KVDL-2010             
295388251  445      Mycodrosophila claytonae             
295388249  445           Drosophila pinicola             
295388247  445         Drosophila macrospina             
295388245  445          Drosophila guttifera             
295388243  445            Drosophila falleni             
295388241  445            Zaprionus indianus             
295388239  445           Zaprionus sepsoides

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fmichonneau commented on September 25, 2024

That looks good!

My only comment looking quickly at the code is that it might be worth using httr::pase_url function to get the doi instead of relying on a sub e.g.

parse_url("http://dx.doi.org/10.1017/S001667231000008X")$path

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Provide integration with other packages for study metadata about rotl HOT 5 CLOSED

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