PathwayCommons / classifier-pipeline

A workflow for classifying articles
MIT License
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Enable access to article 'feed' via web service #26

Closed jvwong closed 2 years ago

jvwong commented 2 years ago

Background: Currently, the classifier analyzes the daily PubMed updates and identifies those containing pathway/interaction information. This information is persisted in a database (RethinkDB). Consequently, this data represents a continuous 'feed' of (some of the) pathway/interaction information added to the literature.

Problem/opportunity: Being stored in a database, it is rather difficult and cumbersome to access (need to dump, restore elsewhere; data is in a particular database/table). This information just as easily be offered as a customizable web feed.

[
  {
    "articleCitation": "Cell Death Dis, 2022",
    "authorName": "Jie",
    "doi": "10.1038/s41419-022-05093-0",
    "emailRecipientAddress": "huangjie@suda.edu.cn",
    "last_updated": "2022-08-09T04:05:50.964Z",
    "pmid": "35902557",
    "pub_date": "2022-07-28T00:00:00.000Z"
  },  
  ...,
  {
    "articleCitation": "Pediatr Surg Int, 2022",
    "authorName": "Rongde",
    "doi": "10.1007/s00383-022-05144-9",
    "emailRecipientAddress": "wrd2190@163.com",
    "last_updated": "2022-08-09T04:04:35.402Z",
    "pmid": "35836014",
    "pub_date": "2022-09-01T00:00:00.000Z"
  }
]

Details: Design-wise, it makes most sense to provide the web service on top of this code, to abstract away the details of the database.