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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