Skip to content

Latest commit

 

History

History
252 lines (208 loc) · 8.69 KB

journalStructure.md

File metadata and controls

252 lines (208 loc) · 8.69 KB

Structure of High IF Journals (Total number: 43)

This document contains the structure of Journals having Impact Factor greater than 15 - taken from 10x Genomics. Only relevant sections from the journals are added.

Programming languages used

  • R
  • Python

Source code found on

  • Github
  • Zenodo

Sequencing Dataset found on

  • European Genome-phenome Archive (EGA)
  • Gene Expression Omnibus (GEO)
  • Sequence Read Archive (SRA)
  • International Nucleotide Sequence Database Collaboration (INSDC)
  • European Nucleotide Archive (ENA)
  • BioStudies: ArrayExpress (Gene expression data)
  • database of Genotypes and Phenotypes (dbGaP)
  • ProteomeXchange Consortium - PRIDE: stores data related to protein and peptide identifications
  • ProteomeXchange Consortium - PeptideAtlas: stores datasets focusing on peptide identifications and their associated spectral evidence
  • ImmPort (Immunology Database and Analysis Portal)
  • Zenodo
  • China National GeneBank DataBase (CNGBdb)
  • BioProject
  • Medical Genomics Japan Variant Database (MGeND)
  • CellxGene
  • National Genomics Data Center (NGDC): Genome Warehouse, Genome Sequence Archive (GSA)
  • The Neuroscience Multi-omic Data Archive (NeMo)

Cell: IF 45.5 (6)

Structure 01:

Resource availability:

Materials availability

Data and Code/Software Availability

  • contains info regarding sequencing data and source code
  • if code unavailable > “This paper does not report original code” (MUST BE ADDED but not always added)
  • code available upon request from authors
  • already-existing SWs and Algorithms used but no unique code generated - found in Key Resources Table
  • ‘original code’
  • ‘unique code’
  • ‘custom code’
  • github link for original source code or custom code generated by using already-existing SW

Structure 02:

Data and Code/Software Availability:

  • contains info regarding sequencing data and source code

Structure 03: (in publications from 04/2011 to 2016)

Accession Numbers

  • mostly written in plain text without a URL

Cell Stem Cell: IF 19.8

(some publications are not publicly accessible)

Resource availability:

Lead contact

  • requests for resources and reagents

Materials availability

Data and Code/Software Availability

  • section not found in several publications
  • sequencing data listed but not source code
  • 'original code'
  • 'novel code'
  • accession numbers of sequencing data & source code URL (Github/Zenodo) listed in Key Resources Table
  • accession number stated in plain text instead of hyperlinks/URLs

Other Cell journals:

  • Cancer Cell: 48.8
  • Immunity: 25.5
  • Cell Host & Microbe: 20.6 (no publication has added source code or accession codes - resources available upon request)
  • Cell Metabolism: 27.7

Nature Immunology: IF 27.7 (14)

Structure 01:

Data availability

  • uploaded on database(s) mentioned above
  • available upon request
  • fasta files found under Supplementary Information as Supplementary Data (observed in only one publication so far)
  • found under Source Data: ‘Fig.’ - .xlsx files

Code availability

  • ‘custom code’
  • ‘custom software’
  • ‘new codes’
  • ‘customized code’
  • not provided
  • available from authors upon request
  • no new code, used existing code

Structure 02:

Accession codes

  • contains URLs to sequencing data

NOTE: before 2019: Accession Codes, in 2019: Data Availability, 2020 onwards: Data Availability, Code Availability

Other Nature journals:

  • Nature Biotechnology: 33.1
  • Nature Medicine: 58.7
  • Nature Genetics: 31.7
  • Nature: 50.5
  • Nature Cell Biology: 17.3
  • Nature Neuroscience: 21.2
  • Nature Cancer: 23.5
  • Nature Methods: 36.1
  • Nature Metabolism: 18.9
  • Nature Biomedical Engineering: 26.8
  • Nature Microbiology: 20.5
  • Cellular & Molecular Immunology: 21.8
  • Nature Nanotechnology: 38.1

The Lancet Microbe: IF 20.9 (3)

Data Sharing

  • contains accession numbers for sequencing data and source code URLs
  • accession numbers stated in plain text instead of hyperlink

Other Lancet Journals:

  • The Lancet Oncology: 41.6
  • The Lancet Infectious Diseases: 36.4

Science: 50.3 (4)

Acknowledgments

Data and materials availability

  • accession numbers in plain text/ links to sequencing data in References (Zenodo URLs)/ hyperlinks
  • source code: hyperlinks, sometimes in References, not available at all
  • several publications are not freely accessible

Science Immunology: IF 19.1

Data and materials availability

  • contains accession numbers for sequencing data and source code URLs

Other Science Journals:

  • Science Translational Medicine: 16.9
  • Science Bulletin: 18.8

Cancer Discovery: IF 30.6

Structure 01:

Data Availability/ Data Deposition/ Data and Software Availability/ Data and Materials Availability/ Data Reporting/ Code Available/ Data Archive (2019-present)

  • contains accession numbers for sequencing data and source code URLs
  • accession numbers stated in plain text instead of hyperlinks/URLs
  • very few publications contain source code

Accession numbers

  • contains accession numbers of publicly available data used by authors

Structure 02:

Methods:

Data Availability

  • information related to sequencing data

Software/Code Availability

  • source code

Nucleic Acids Research: IF 16.6

Data Availability

  • contains information regarding sequencing data
  • few publications mention source code

Cell Research (Nature): IF 28.2

Data Availability/ Data Access

  • very few mentioned source code
  • accession numbers stated in plain text instead of hyperlink

Gastroenterology: IF 25.7

Data availability statement

  • contains accession codes and source code

Gut: IF 23.0

Data availability statement

  • contains accession codes (plain text) and source code (2 out of 13 publications)

Circulation: IF 35.5

Independent Data Access/ Data Availability/ Methods/ Data Resources

  • accession codes (plain text)
  • source code found (1 out of 23 publications)
  • available upon request

Neuro-oncology: IF 16.4

Data Availability

  • contains info regarding sequencing data and source code (1 out of 4 publications)

Signal Transduction and Targeted Therapy: IF 40.8

Structure 01:

Data Availability

  • accession number/acession code/project number found in plaintext instead of hyperlink
  • source code available upon request or not available at all - available on Github for only 1 out of 23 publications

Structure 02:

Data Availability

Code Availability

Bioactive Materials: IF 18.0

Data availability/ Availability of data and materials/ Data and materials availability

  • 1 out of 7 publications stated accession number
  • data available upon request
  • no data available at all
  • no source code

Annals of the Rheumatic Diseases: IF 20.3

Data Availability Statement:

  • only accession numbers found (2/5 publications) - no source code
  • available upon request
  • section not found

National Science Review: IF 16.3

Data Availability

  • accession numbers stated in plaintext
  • code available upon request or not available at all

Molecular Cancer: IF 27.7

Data Availability/ Availability of data and materials

  • accession numbers in plain text
  • data available upon request
  • source code not available for any publication

Journal of Hepatology: IF 26.8

Structure 01:

Data Availability Statement

  • accession numbers stated in plain text
  • source code URLs stated (1 out of 19 publications)
  • available upon request

Structure 02:

Data Availability Statement

Code Availability

Journal of Hematology and Oncology: IF 29.9

Availability of Data and Materials

  • data available upon request
  • 1/4 publications stated sequencing data accession number (plain text)
  • no source code found

Military Medical Research: IF 16.7

Availability of data and materials

  • 3/4 publications contain accession numbers
  • 1/4 publication's data is available upon request

Molecular Neurodegeneration: IF 15.1 (16)

Availability of data and materials

  • data available upon request
  • 1/7 publication shared source code URL
  • 1/7 publication shared correct accession number with name of the Database

General Observation: Most publications started adding source code from 2019 onwards

ISSUES WITH 10xGenomics:

  • results show around 8000 articles but scrapes only 999 articles
  • search hits go till page 50, each page contains 20 articles
  • faulty sorting: ascending starts from 1880 and goes till 2019 (page 50), descending starts from 2024 and goes till 2023 (page 50)