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Add parser for PubMedCentral full texts #154

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caufieldjh opened this issue Jul 12, 2023 · 5 comments
Closed

Add parser for PubMedCentral full texts #154

caufieldjh opened this issue Jul 12, 2023 · 5 comments
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enhancement New feature or request

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@caufieldjh
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We'd like to work with larger sets of full texts from PubMed (Central).
These may be downloaded here: https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/
But we still need functions to:

  1. Index PMC docs
  2. Retrieve texts for a list of PMIDs
  3. Pass segments of full texts to extract function (assuming the full doc will be longer than context length) - ideally filterable by some segment, or defaulting to the first n tokens or so
@justaddcoffee
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Access to full text of articles would help with both KG-IBD and Jens/Ravi's kidney project

@caufieldjh
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In the short term, I can add functionality to retrieve PMC XML through the API for corresponding PMIDs, as available

@justaddcoffee
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yep, I guess accessing through the API for now would be the quickest solution

@caufieldjh
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This is complete; see #156

@caufieldjh
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and by complete I mean "through the API", not "downloaded and indexed", but we can re-open this if that becomes necessary

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