## CZI Software Mentions

[Link](https://github.com/chanzuckerberg/software-mentions)

Source:
- biomedical papers
  - 2.4 million papers from NIH PubMed Central commercial subset
  - 1.4 million papers from NIH PubMed Central non-commercial subset
  - 4 million papers from CZI Publishers' collection
    - biomedical, but also some other areas
    - includes 1.7 million PubMed Central papers

Method:
- SciBERT extracts plain-text software mentions
- disambiguation of mentions using DBSCAN
- linking by exact-match query in Pip, SciPy, GitHub
  - GitHub links have high error / unclear rate in evaluation

Content:
- software mentions
- context (2-3 lines)
- disambiguated software name
- link (if any)

## PLOS Open Scence Indicators

[Link](https://plos.figshare.com/articles/dataset/PLOS_Open_Science_Indicators/21687686)

Source:
- 61,000 research articles published in PLOS (2019-2022)
- 6,500 articles in non-PLOS journals (for comparison)

Method:
- analyse XML of published research articles
- detect 3 OpenScience practices
  - sharing of research data (NLP, DataSeer)
  - sharing of code (NLP, DataSeer)
  - posting of preprints (CrossRef, DataCite)

Content:
- data and code generation and sharing rate
- location of shared data and code

## Softcite dataset

[Link](https://github.com/howisonlab/softcite-dataset)

Source:
- 5,000 open access research publications in life sciences and social sciences

Method:
- manually annotated (I think)

Content:
- XML publications with encoded annotations (used GROBID)
- later used to train ML models
  - implemented in GROBID module for software mention recognition

## SoftwareKG

[Link](https://data.gesis.org/softwarekg/)

Source:
- SoftwareKG_Social: 51,000 articals from social sciences
- SoftwareKG_PubMed: 3M PubMed Central articles

Contents:
- knowledge graph
- name of software mention
- accessibility, URL, license, disambiguation

## French Open Science Monitor

[Link](https://barometredelascienceouverte.esr.gouv.fr/software/general), [Methodology Paper](https://github.com/Barometre-de-la-Science-Ouverte/bso3-techdoc/blob/master/methodology/bso3.pdf)

- select relevant papers using affiliation detector for CrossRef
  - identifies papers with at least one French author
  - uses controlled list of institutions for France
- run Grobid, then software mention detection + dataset mention detection on the collection

## SoMeSci

[Paper](https://peerj.com/articles/cs-835/), [data](https://data.gesis.org/somesci/)

Source:
- 1367 PubMed Central papers

Contents:
- Knowledge graph
- version, developer, URL, citations