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PubMed Central support #3918

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reckart opened this issue Apr 4, 2023 · 0 comments
Closed

PubMed Central support #3918

reckart opened this issue Apr 4, 2023 · 0 comments
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@reckart
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⭐️ Enhancement New feature or request Module: External Search Module: PubMed/PMC
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28.0

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@reckart
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reckart commented Apr 4, 2023

Is your feature request related to a problem? Please describe.
INCEpTION can already access PubAnnotation, but this misses for example metadata such as titles of publications in the search results. It would be nice to have a similar direct access to e.g. PubMed Central.

Describe the solution you'd like
Add a new external search provider for PubMed Central.
@reckart reckart added this to the 28.0 milestone Apr 4, 2023
@reckart reckart self-assigned this Apr 4, 2023
@reckart reckart added this to 🔖 To do in Kanban via automation Apr 4, 2023
reckart added a commit that referenced this issue Apr 4, 2023
@reckart
#3918 - PubMed Central support
44bf84f 
- Basic PubMed Central support as external search
- Very basic and experimental BioC support
- Use Entrez to augment search results from PubAnnotation, e.g. so we can display titles
- Improve visuals of the external search page
reckart added a commit that referenced this issue Apr 5, 2023
@reckart
#3918 - PubMed Central support
7eeb6fe 
- Fix JavaDoc reference
reckart added a commit that referenced this issue Apr 6, 2023
@reckart
#3918 - PubMed Central support
22dbf23 
- Fix JavaDoc reference
reckart added a commit that referenced this issue Apr 11, 2023
@reckart
#3918 - PubMed Central support
8a390b9 
- DKPro Core 2.3.0 -> 2.3.1
- Sort results by relevance which is the same as on the PubMed website
- Avoid including results from the last 24 hours to reduce the risk that BioC documents are not available for them
- Better support for annotations in BioC documents
- More testing
reckart added a commit that referenced this issue Apr 12, 2023
@reckart
#3918 - PubMed Central support
4f610b7 
- DKPro Core 2.3.0 -> 2.3.1
- Sort results by relevance which is the same as on the PubMed website
- Avoid including results from the last 24 hours to reduce the risk that BioC documents are not available for them
- Better support for annotations in BioC documents
- More testing
reckart added a commit that referenced this issue Apr 12, 2023
@reckart
#3918 - PubMed Central support
3094cd3 
- DKPro Core 2.3.0 -> 2.3.1
- Sort results by relevance which is the same as on the PubMed website
- Avoid including results from the last 24 hours to reduce the risk that BioC documents are not available for them
- Better support for annotations in BioC documents
- More testing
reckart added a commit that referenced this issue Apr 13, 2023
@reckart
#3918 - PubMed Central support
c0adfb7 
- DKPro Core 2.3.0 -> 2.3.1
- Sort results by relevance which is the same as on the PubMed website
- Avoid including results from the last 24 hours to reduce the risk that BioC documents are not available for them
- Better support for annotations in BioC documents
- More testing
reckart added a commit that referenced this issue Apr 14, 2023
@reckart
Merge pull request #3919 from inception-project/feature/3918-PubMed-C…
4cb72ae 
…entral-support

#3918 - PubMed Central support
@reckart reckart moved this from 🔖 To do to 🏃‍♀️ In progress in Kanban Apr 14, 2023
reckart added a commit that referenced this issue Apr 15, 2023
@reckart
#3918 - PubMed Central support
f61a39a 
- Fix test
reckart added a commit that referenced this issue Apr 15, 2023
@reckart
Merge branch 'main' into feature/3944-Ability-to-use-recommenders-as-…
6b4ddc2 
…curator

* main:
  #3918 - PubMed Central support
reckart added a commit that referenced this issue May 23, 2023
@reckart
#3918 - PubMed Central support
2903d83 
- Added documentation for PMC external repo
- Added documentation for BioC format
reckart added a commit that referenced this issue May 23, 2023
@reckart
Merge pull request #4013 from inception-project/feature/3918-PubMed-C…
ebf9eb4 
…entral-support

#3918 - PubMed Central support
@reckart reckart closed this as completed May 23, 2023
Kanban automation moved this from 🏃‍♀️ In progress to 🍹 Done May 23, 2023
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@reckart reckart

Labels
⭐️ Enhancement New feature or request Module: External Search Module: PubMed/PMC
Projects
Kanban
  
🍹 Done
Milestone
28.0
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@reckart