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Co-occurrence of Cell Lines, Basal Media and Supplementation in the Biomedical Research Literature Cover

Co-occurrence of Cell Lines, Basal Media and Supplementation in the Biomedical Research Literature

Journal of Data and Information Science
Volume 5 (2020): Issue 3 (August 2020)
By: Jessica Cox,  Darin McBeath,  Corey Harper and  Ron Daniel  
Open Access
|Jul 2020

Figures & Tables

Figure 1

Trends in top 5 basal media mentions since the year 2000.A: We plotted the unique document count of our top 5 medias (DMEM, RPMI, MEM, F12, DMEM/F12) over time, from 2000–2018, to observe changes in counts over time. Most articles published referenced DMEM. B: We plotted the compound annual growth rate (CAGR) of the number of mentions from 2000–2018. The media curves are plotted in black, and as a baseline, the CAGR of all full length articles published in the same journals was is plotted in gray. Articles grew at a rate of 5.3% over the 18 year period. DMEM/F12 had the highest growth rate, around 21%, while the others maintained between 10–18.
Trends in top 5 basal media mentions since the year 2000.A: We plotted the unique document count of our top 5 medias (DMEM, RPMI, MEM, F12, DMEM/F12) over time, from 2000–2018, to observe changes in counts over time. Most articles published referenced DMEM. B: We plotted the compound annual growth rate (CAGR) of the number of mentions from 2000–2018. The media curves are plotted in black, and as a baseline, the CAGR of all full length articles published in the same journals was is plotted in gray. Articles grew at a rate of 5.3% over the 18 year period. DMEM/F12 had the highest growth rate, around 21%, while the others maintained between 10–18.

Figure 2

Trends in top 10 cell line mentions since the year 2000.A: We plotted the unique document count of our top 10 cell lines (HEK293, HEK293T, HeLa, Hep-G2, MCF-7, MDA-MB-231, NIH 3T3, RAW 264.7, SH-SY5Y, THP-1) over time, from 2000–2018, to observe changes in counts over time. Most articles published referenced HEK293, HEK293T or HeLa. B: We plotted the compound annual growth rate (CAGR) of the number of mentions from 2000–2018. The cell line curves are plotted in black, and as a baseline, the CAGR of all full length articles published in the same journals is plotted in gray. Articles grew at a rate of 5.3% over the 18 year period. HEK293T cells had the highest growth rate of 24.2%.
Trends in top 10 cell line mentions since the year 2000.A: We plotted the unique document count of our top 10 cell lines (HEK293, HEK293T, HeLa, Hep-G2, MCF-7, MDA-MB-231, NIH 3T3, RAW 264.7, SH-SY5Y, THP-1) over time, from 2000–2018, to observe changes in counts over time. Most articles published referenced HEK293, HEK293T or HeLa. B: We plotted the compound annual growth rate (CAGR) of the number of mentions from 2000–2018. The cell line curves are plotted in black, and as a baseline, the CAGR of all full length articles published in the same journals is plotted in gray. Articles grew at a rate of 5.3% over the 18 year period. HEK293T cells had the highest growth rate of 24.2%.

Figure 3

Co-occurrence of cell line and basal media.Each bar represents the total number of sentences that mentioned the cell line (x-axis), broken down by count that referenced a specific basal media. Note that DMEM is the dominant media in all but one cell line. THP-1, an immune-type cell, is the only cell type to occur most frequently with RPMI, a media developed for these cell types.
Co-occurrence of cell line and basal media.Each bar represents the total number of sentences that mentioned the cell line (x-axis), broken down by count that referenced a specific basal media. Note that DMEM is the dominant media in all but one cell line. THP-1, an immune-type cell, is the only cell type to occur most frequently with RPMI, a media developed for these cell types.

Figure 4

Co-occurrence heatmap of cell line, basal media and supplement tokens.In this figure, the values represent the raw count of sentences that contain that combination of words (cell line, basal media and supplement token). The shading represents the percent of the total sentences within that pane, which is defined by media, in the left column.
Co-occurrence heatmap of cell line, basal media and supplement tokens.In this figure, the values represent the raw count of sentences that contain that combination of words (cell line, basal media and supplement token). The shading represents the percent of the total sentences within that pane, which is defined by media, in the left column.

Document level count of top 10 cell lines and their representation in sentences mentioning a cell line and basal media_

Cell lineCount of unique documents that have a cell line and media co-occurPercentage of documents that have a cell line and media co-occur (n = 12,732)CAGR (2000–2018)
HEK293T1,31410.3%20.7%
HeLa1,2209.6%11.2%
HEK2938486.7%24.2%
MCF-77716.1%14.9%
Hep-G25234.1%16.2%
MDA-MB-2314903.9%22.9%
THP-13743%23.1%
RAW 264.73582.8%20.1%
NIH 3T33422.7%10.2%
SH SY5Y3352.6%19.8%

ATCC Cell Culture recommendations for the 10 most frequently occurring cell lines in our corpus_

Cell LineSpecies and cell type Recommendedbasal mediaRecommended supplementsMost frequently co-occurring basal media
HEK293Homo sapiens, embryonic kidneyMEM10% FBSDMEM
HEK293THomo sapiens, embryonic kidneyDMEM10% FBS, 2 mM l-glutamineDMEM
HeLaHomo sapiens, cervix, epithelialMEM10% FBSDMEM
Hep-G2Homo sapiens, liver, epithelialMEM10% FBSDMEM
MCF-7Homo sapiens, mammary glands, epithelialMEM10% FBS, 0.01 mg/ml insulinDMEM
MDA-MB-231Homo sapiens, mammary glands, epithelialL-1510% FBSDMEM
NIH 3T3Mus musculus, embryo, fibroblastsDMEM10% FBSDMEM
RAW 264.7Mus musculus, monocyte/macrophageRPMI10% FBSDMEM
SH-SY5YHomo sapiens, bone marrow, epithelialMEM:F1210% FBSF12
THP-1Homo sapiens, peripheral blood, monocyteRPMI0.05 mM 2-mercaptoethanol, 10% FBSRPMI

Document level count of top 5 basal medias and their representation in biomedical research mentioning cell cultured published since 2000_

Basal mediaRaw annotation counts (n = 126,409)Count of unique documents that mention mediaPercentage of documents that mention media (n = 26,036)CAGR (2000–2018)
DMEM40,34715,77060.6%13.4%
RPMI36,4908,11431.2%9.2%
MEM17,1545,36920.6%10.4%
F129,4133,66014.1%15.4%
DMEM/F129,6042,2218.5%21%

Raw count of top 10 noun tokens following basal media mentions and their proportion of sentences describing cell culture conditions_

TokenRaw countProportion of sentences mentioning cell and media n = 12,732
serum10,68583.9%
fbs9,28372.9%
penicillin4,70837%
streptomycin4,63236.4%
l-glutamine2,73921.5%
fcs2,59820.4%
calf2,49719.6%
penicillin-streptomycin1,66713%
antibiotic1,2329.7%
acid1,2179.6%
DOI: https://doi.org/10.2478/jdis-2020-0016 | Journal eISSN: 2543-683X | Journal ISSN: 2096-157X
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Language: English
Page range: 161 - 177
Submitted on: Jan 31, 2020
Accepted on: Apr 23, 2020
Published on: Jul 3, 2020
Published by: Chinese Academy of Sciences, National Science Library
In partnership with: Paradigm Publishing Services
Keywords:
Cell culture,
Biomedical research,
Text mining
Related subjects:
Computer sciences,
Information technology,
Project management,
Databases and data mining

© 2020 Jessica Cox, Darin McBeath, Corey Harper, Ron Daniel, published by Chinese Academy of Sciences, National Science Library
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

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