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SciScraper

--WORK IN PROGRESS--

The goal of this project is to create an efficient means of gathering as much scientific data as possible on a given topic. Legally, this limits the scope of the scraper to a handful of databases that fit this criteria, such as PubMed Central. Pertinent information such as abstracts, conclusions, and figures can then be concatenated into an database. These can then be converted into HTML for viewing, PDF for printing/sending, or perhaps some sort of interactive JS navigation.

The databases used will be those outlined by Unpaywall as open-access: PubMed Central, the DOAJ, Crossref (particulary their license info), DataCite, Google Scholar, and BASE. Currently only utilizing PubMed Central

At the moment, reports can be generated in markdown, and HTML. Working on LaTeX and PDF.

Similar projects:

https://github.com/ContentMine/journal-scrapers (for ContentMine framework)

https://github.com/EFavDB/PubmedCentral_Scraper (in R, only from PubMed)

Hosted Version

Using the Scraper

The scraper takes up to three arguments: a main topic, optional queries, and the maximum number of results to return. It is initialized by running sciscraper() from Main.py, and generates a dictionary with results. There is an included SQL table generator that can be called with the sql_insert(mainDict) from Main.py, but this is not currently in use by default or within the webapp. Markdown/HTML/PDF versions of the report can also be generated (from the ReportGenerator.py functions). A local web interface can be run with Flasker.py, and accessed via the standard http://127.0.0.1:5000/. This is presented with Bootstrap and is what is currently hosted in the webapp at http://sciscraper.pythonanywhere.com.

Function Documentation

1 - PubMed Central API

The documentation here provides an overview for how to interact with the PMC database with 9 different utilities. Search terms are parsed left to right, using capital Boolean operators that are parenthetically encapsulated. For example, to search for the main topic of ‘salmonella’ and one of multiple queries (e.g. eggs or beef) it would be typed “salmonella AND (protein OR amino)”.

The user input to the scraper will inherit this method of searching a main topic in additional to optional queries. ESearch can be used initially to query the database, then EFetch/ESummary to retrieve the articles’ information. Image scraping is done using BS4.

To Do

  • Curtailing long sections/'anthology' articles (scrape +2 nResults as buffer?)
  • Download HTML/PDF feature (email?)
  • Interaction?
  • Popular searches
  • Faster
  • Sidebar nav of studies?
  • Additional DB's - arXiv, etc.
  • Large-scale analytics with bootstrap cards UI?