Visualization of life science research by using MeSH and GIS techniques
Masashi Shirabe
This work is done as a part of the project “Scientometrics conducive to management of funding programs”, which supported by JST/RISTEX.e of funding programs
Summary
• By using MeSH, academic papers in life science field have been mapped.– Research topics are mapped in reasonable positions.– Research topics and fields on the maps can be interpreted even
by non-specialists– Micro, meso, and macro maps are available.
• By using GIS techniques, some information can be overlaid on such maps. As its result, quality and quantity indicators as well as categories are visualized.
• Please give your comments on…– How could you use these maps in your operations?– How can we improve the maps?– What type of indicators should be overlaid on the maps?
On data
• academic papers– intersection of the following two datasets
• articles, reviews, notes, letters, and article & proceedings papers in WoS ( SCI Ex )
– DBYs are 1992-2011
• records on PubMed database– Publication years are 1991-2012
– Top m% cited papers are identified by our original program
• patent data– utility patents registered to USPTO between 1992-2012.– paper citations (i.e., science linkages) are identified by our
original program (http://link.springer.com/article/10.1007%2Fs11192-014-1293-8).
A result of mapping life science research (macro map)
A result of mapping life science research (macro map)
nursing, health care
psychiatric medicine, behavioral science
neuroscience
diagnosis, treatment
metabolism, biochemistry
molecular biologyenzyme,
protein
diseasegerm, virus,
infectionimmunology
stem cell
pharmacology
pathology
plant science
drug, physiology
related science
environment,ecology
materials
public health
sequence homogeneity
unclear regions
analytical chemistry
Change of number of papers published in the world (2000-11)
量 Increase rapidly in all the fields世
Intertemporal Comparison
2000 (moving average) 2010 (MA)
量 psychiatric medicine, behavioral science, physiology / diagnosis technology, system biology, analytical chemistry … UP
世
Change of number of papers published in Japan (2000-11)
量 stagnation (unchanged)日
Intertemporal Comparison
2000 (MA) 2010 (MA)
量 sequence homogeneity … DOWN
physiology / diagnosis technology, system biology, stem cell research … UP
日
Change of shares of Japanese papers (2000-10)
比率
general declines日
Intertemporal Comparison
2000 (MA) 2010 (MA)
比率 日
Change of relative numbers of papers cited by US patents
Registered between 2001 and 11
量Basic research papers are
highly cited 世
Intertemporal Comparison
2001 2011
量diagnosis technology,
theoretical model … UP
sequence homogeneity … DOWN
世
Change of share(Japanese papers cited by patents / all paper cited by patents)
Registered between 2001 and 11
質Shares are increasing (legacy of the past)
日
Intertemporal Comparison
2001 (MA) 20 11 (MA)
質 日
Change of share (patent citations of Japanese papers / that of the world)
Registered between 2001 and 11
比率 日
Intertemporal Comparison
2001 (MA) 2011 (MA
比率 日
Implications
• In life science– Number of papers in the world has steadily increased.– Although Japanese shares in most field were over
10% around 2000, they has declined just over 6 %.– In terms of citations by patents, physiology, diagnosis
technology, system biology gained attentions recently.– Both citations and number of cited papers in Japan
increased recently. (legacy of the past)
What we have done: Developed research platform
• Database combined SCI Ex and PubMed
PubmedSCI Ex
( WoS )linked
MeSH• structured• relatively easy to
interpret
Funding info.
citation-> evaluation
acknowledgement
affiliation-> international, sector, institutional analysis
USPTOIPC,PCT-> tech field…
cite
From 12 million PubMed records, 8.5 million records are linked to SCI Ex records.
inte
rpre
tabl
e
expr
essio
n
Scope of our project
biblio info (SCI, US patents, PubMed)
Macro/micro map
NIH funding
evaluation by citation info and visualization of
citation
evaluation of contribution to
innovation (science linkage
analysis)
evaluation of funding
programs by acknowledge
Networking triggered by NIH
funding programs
Overall visualization
Scope of our project
biblio info (SCI, US patents, PubMed)
Macro/micro map
NIH funding
evaluation by citation info and visualization of
citation
evaluation of contribution to
innovation (science linkage
analysis)
evaluation of funding
programs by acknowledge
Networking triggered by NIH
funding prgorams
Overall visualization
Presented in this file
macro: life sciencemicro: pluripotent stem cell research
ライフサイエンスother visualizations of life science research
Mapping by the second level descriptors
Easy to interpret, luck of detail information
mapping by second level descriptor X qualifier
perfectly understandable, but retandatnt
It remains unanswered which mapping methods are better in application.
Distribution of life science paper in the world
量 世
Distribution of Japanese life science papers
量Weak in left hand side (clinical medicine and related fields)
日
Japanese share
比率 日
number of Japanese Top 1% cited papers
量 Basic research!日
Japanese share in Top 1% cited papers
世界平均
質 日
Japanese share in Top 10% cited papers
世界平均
質 日
Average citations by US patents (per paper)
質 basic research papers are cited世
Japanese share in papers cited by US patent
世界平均
質 日
Japanese share of citations by US patents
世界平均
質 日
Implications
• Basic research papers are more published in the world.• In comparison to the world, Japan has been focused on
basic research.– This phenomena are partially explained by the fact that clinical
papers, especially case report papers by Japanese physicians are likely to be published in Japanese journal.
• Basic research papers are more cited by US patents.• Japanese papers in health care and drug, biochemistry
are relatively cited.• Ration of top 1% / 10% cited Japanese papers to all
Japanese papers are lower than its world average.
Japanese papers with public funding (2010)
量 Protein!日
Breakdown (2010)
Grants-in-aid MHLW Grants
量 日
Breakdown (2010)
JST NEDO (of METI)
量 日
Share of publically funded papers (2010)
比率 日
Share of papers funded by Grants-in-aid
比率 日
Share of papers funded by MHLW Grants
比率 日
Shares of papers funded by JST
比率 日
Share of papers funded by NEDO
比率 日
Share of Grants-in-aid – Share of MHLW Grants
比較 日
Implications
• In terms of quantity, public research funds are contributing to paper productions in basic research.– In terms of research quality…
• Each funding agency has its specific funding pattern, which fits its role.
• However, judging from output indicators, public supports to clinical research and disease research seem insufficient.– Who pays currently ? Private companies?
Pluripotent stem cell research
Mapping of Pluripotent stem cell research
Mapping of Pluripotent stem cell research
ES cells
iPS cell
tissue eng.
mesenchymal SC
culture
regenerative mdeicineembryo research
nerve
embryonic carcinoma cell
osteoplastic cell
gene transfection
Experimental Animals
RT-PCRbase sequence
unclear areas
pluripotent SC
Number of Pluripotent stem cell research papers in the world
量 世
Change of number of Pluripotent stem cell research papers in the world (2000-10)
量 世
2000-2010 ( 3 年移動平均)
Change of number of Pluripotent stem cell research papers cited by US patent
absolute number relative number
量 世
2001-2011 年登録特許( 3 年移動平均)
Japanese share of Pluripotent stem cell research papers
比率
高い世界シェア日
Change of Japanese share of Pluripotent stem cell research papers
比率
2005 年以前は論文数が少なくノイズが多い。
日
2000-2010 ( 3 年移動平均)
Intertemporal Comparison
2005 2010
比率 日
Japanese share of top 1 % cited papers
世界平均
質In ES and iPS research, the shares are similar to world averages.日
Japanese share of top 10 % cited papers
世界平均
質 日
Japanese Share of papers cited by US patents
Attention to legend ->
質 日
Change of papers cited by patents by registered years
質 日
2001-2011 (MA)
Pluripotent stem cell research papers funded publically in Japan
量 日
Share of pluripotent stem cell research papers funded publically in Japan to all Japanse pluripotent stem cell research papers
貢献 日
Funded by Grants-in-aid
number share
比率量 日 日
JST
number share
比率量 日 日
MHLW Grants
number share
比率量 日 日
NEDO (of METI)
number share funded projects are identified
比率量 日
日
Future research• Technical problems
– mapping parameter– improve two dimensional expression
• Overlaid information– funding information
• money..– funded institution– science linkages may show different patters by IPCs…– Comparisons to NIH funding
• meso level mapping– mapping by the 4th or 5th level descriptors
• more detailed micro maps (for supporting researchers’ activity)• Cope with (real and potential) users’ request
RISTEXSCIENTOMETRICSPJ[AT]GOOGLEGROUPS.COM
Thank you!
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