The Digital Botanical Garden Initiative
Follow-up by Donat #11
Replies: 9 comments 5 replies
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One more thing: could you provide me with 5 articles each of J Nat Prod and Phytochemsitry that you also will use for the exemplar annotations of chemical and other elements, that would be helpful. We then process them right away so we can use them for the JATS conversion work on our side. Donat |
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Hi Donat, The bibliographical metadata is available here : zenodo.org/record/7534077 (reference_metadata.tsv.gz) all fields should be self-explanatory. In case, I pre-treated it to fulfill your request: We have: • 161130 DOIs Of course, this is very far from the full corpus of each journal. You will find attached: • the full table with the fields you requested I’ll coordinate with PM for the 5 demo articles and will let you know. |
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With the file: references.tsv.gz |
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And the table:
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Thanks for this comprehensive list. I have been looking at some Phytochemistry articles used to discuss the project at its inception. When I look at other eg Tetrahedron, it seems that they are not description of metabolome, but their use to create derivatives and other application, not primarly the description of novel substances? Also we should define a corpus that includes the pairs Following our discussions, most of such pairs are in |
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Indeed I think we should focuss first on JNP and Phytochemistry, which should mostly focuss on the description of novel compounds (structure, occurences, biological activities). Tetrahedron reported, historically, novel occurences but it is rather an organic chemistry focussed paper. |
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So in the previous zenodo.org/record/7534077 you can find all papers in LOTUS so I guess these should ideally be the first filter (in order not to be included) when launching the parsing. |
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We can't download the JNP for scraping, because HESG and UNI Geneva is not part of the Swiss consortium sharing access - Uni Neuchâtel would be. The question is, how we could get all those files, or at least the one for the last couple of years. it seems we have access via HESG to Phytochemistry. |
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OK. I have asked IT here for a UniFr account for you I will keep you posted. Let's keep this as a point for the next meeting. |
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here it is |
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@oolonek, the scraping is complex - Elsevier makes it very tedious and near to impossible. Might it be possible on your side to get a student just to download the last couple of years of JNatProducts and Phytochemistry to start with? We still try to find a way to scrape though, but no t clear whether we are able to make it. If so, let's discuss the file naming system Also, might it be possible to incldue @flsimoes into this discussion, who is running the production on our end. cheers |
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We usually have the file names set as Examples: |
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@tkuhn For a bit of context |
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Hi PM and Adriano
Just a first follow-up of the LOTUS BiCIKL meeting.
Adriano, you mentioned that you have a bibliography of the articles cited in LOTUS. Might it be possible to get this in form of a spreadsheet, which include the journal names, the publication year in separate fields so we can have a look at the diversity of the journals you cover?
For Phytochemistry and the Journal of Natural Products, lets find out how many articles there are, how many are included in LOTUS so we get an idea of how many to be processed.
If somebody on your side would have a couple of hours to look at the articles and see, whether a journal has one style over the last 20 years, or when the style changed, that would also be helpful.
On our side, we will look into getting all the pdfs
Cheers
Donat
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