Novoseek presentation to the scientist at the Molecular Biology Reseach Institute Severo Ochoa.

1. Pasado, presente y futuro
de la búsqueda de literatura científica
Ramón Alonso-­Allende

2. y futuro
Pasado, presente
de la búsqueda de literatura científica
Ramón Alonso-­Allende

3. ëÉ~êÅÜ êÉ~Ç
Future
Science Cicle
Search =
Today
Integration + Meaning + Social
ïêáíÉ ÉñéÉêáãÉåí
Relevance
Value system
2000’s
1990’s
+ Complete
+ Easy
-­ Time

4. Sistemas de información
1995 2000 2005 2010

6. Searches in PubMed
1.000.000
Searches (1000s)
750.000
500.000
250.000
0
1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008

7. Retos

8. Retos
‣ Manejar cantidades ingentes de información.
‣ Ambigüedad del lenguaje.
‣ Tiempo.
‣ Mantenerse al día.
jordinho_dp

9. Mucha información heterogenea
80.000.000
60.000.000
40.000.000
20.000.000
0
92
93
94
95
96
97
98
99
00
01
02
03
04
05
06
07
19
19
19
19
19
19
19
19
20
20
20
20
20
20
20
20
GB PDB Medline SwissProt

10. 43% Genes humanos
tienen nombres ambiguos

11. Algunos datos
Número de términos
4.000
‣ 5.892 términos pueden ser
genes o enfermedades 3.000
‣ 3.963 nombres hacen 2.000
referencia a 2 genes 1.000
diferentes
0
‣ Un término hace referencia 2 3 4 5 6 7 8 9
Número de conceptos
a 114 genes
Disease Genes
Drugs

12. Algunos Ejemplos
sps AAt1
stiff-­man syndrome annuloaortic ectasia
(Diseases or Syndromes) (Diseases or Syndromes)
polystyrene sulfonate alanine aminotransferase
(Pharmacological substances) (Genes and Proteins)
systolic blood pressure
(Biological functions)
spermine synthase
(Genes and Proteins)

13. Language ambiguity
póåoåóãë eoãoåóãë ^Åêoåóã
RÉÇìÅÉ=ïoêÇ=
aáÑÑÉêÉåí=ïoêÇ=Ñoê=íÜÉ= p~ãÉ=å~ãÉ=Ñoê=ÇáÑÑÉêÉåí=
êÉéêÉëÉåíáåÖ=~=
ë~ãÉ=ÄáoãÉÇáÅ~ä=Éåíáíó ÄáoãÉÇáÅ~ä=ÉåíáíáÉë
ÄáoãÉÇáÅ~ä=Éåíáíó
póãÄoä=m^m=áë=~å=~äá~ë=
• få=eìã~å=íÜÉêÉ=~êÉ=~í=
ÑoêW
äÉ~ëí=RKQNU=ÖÉåÉë=ïáíÜ=
•m^m=Em~åÅêÉ~íáíáëJ p`q=ëí~åÇë=ÑoêW
ëóåoåóãë=EPUB=oÑ=íÜÉ=
~ëëoÅá~íÉÇ=éêoíÉáåF • píÉã=`Éää=qê~åëéä~åí
íoí~ä=ÖÉåoãÉF
• jRmpPM=EjáíoÅÜoÇ= • pÉÅêÉíáå
• aêìÖë=Ü~îÉ=~=
êáÄoëoã~ä=éêoí=PMëF • p~äãoå=Å~äÅáíoåáå
ÅoããÉêÅá~ä=å~ãÉ=~åÇ=~=
• m^mli^=Emoäó^=
ÅÜÉãáÅ~ä=å~ãÉ
éoäáãÉê~ëÉ=~äéÜ~F

14. Inmanejable
‣ More than 25 MM documents considering scientific
articles, grants, biomedical patents… relevant sources of
information for biomedical researchers.
‣ 2,000 new scientific papers published everyday
‣ 5 years to read the new scientific material produced
every 24 hours.
‣ Scan 130 journals and read 27 articles per day to follow a
single disease, like breast cancer.

15. Mantenerse al día
‣Alertas en buscadores
‣emailling eTOCs
‣Feeds RSS

16. Search tasks & Lab work by discipline
80%
70%
60%
% time
50%
40%
30%
20%
10%
0%
All
Biochemestry
Mol. & Cell Biol.
Genetics
Biotechnology
Bioinfromatics
Medicine
Other
Searchin literature Searching data form DB Working in the lab
Roos, A., Kumpulainen, S., Järvelin, K and Hedlund, T. (2008). "The information environment of researchers in molecular medicine" Information Research, 13(3) paper 353.
[Available at http://InformationR.net/ir/13-­3/paper353.html]

17. Cómo afrontamos retos

18. Afrontamos los retos:
‣ Integrando información para el usuarios.
‣ Analizando el texto (text mining).
‣ Funcionalidad útil.
‣ Tecnología + Interfaz sencillo = - Tiempo

19. Integración de datos
Sequence DBs Pathway DBs Other DBs
UniProt KEGG Affymetrix
GenBank EC GO
RefSeq Reactome PDB
PIR MIM
EMBL Domain DBs CCDS
Entrez Protein Pfam HPRD
UniSTS PROSITE HGNC
SMART
Gene DBs ProDom
GDB InterPro
Ensembl
Entrez Gene
UniGene
H-­InvDB
MGC
HGNC

20. Text mining
Gene: GH1 Gene: GG1
Growth Hormone 1 Gamma Glutamyl Hydrolase
GeneID: 2688 GeneID: 8836
Synonym: GHN Synonym: conjugasa
Synonym: GH Synonym: GH
adenoma (0.300) antifolate (2.850)
adipocyte (0.418) carboxypeptidase (12.618)
adipose (0.324) folate (0.674)
age-related (0.442) gamma-glu-x (15.452)
genotropin (19.368) antifolylpoly-gamma-glutamate (12.054)

21. Datos indexados
Medline Open access Proyectos I+D
abstracts Texto completo abstracts
NU=j NQRKMMM NIR=j
[=OMM=j=êÉä~ÅáoåÉë
[=Qj=ÅoåÅÉéíoë

22. Comparison: Use-­Case:
Looking for the gene SCT
PubMed: SCT is Solid-­ Cystic tumor
Google Scholar: SCT is name of author
novo|seek: SCT is
meaning you are looking for:
-Secretine
-Stem Cell transplantation

23. novo|seek vs. Google Scholar
dooÖäÉ=pÅÜoä~êW=åo=ï~ó=ío=ÑoÅìë=íÜÉ=ëÉ~êÅÜ=ÄÉóoåÇ=êÉ~ÇáåÖW=
íáãÉJÅoåëìãáåÖ

24. Techonology
‣ Search more efficiently.
‣ Extract more information.
‣ Put into relation different sources of information
‣ Gain time
Semantic Search
Discovery
Concept relations
Knowledge Extraction
by L cornide

25. Semantic Search
‣ Conceptual search
e.g. Search of breast cancer
Detection of breast carcinoma cells in effusions is associated with rapidly fatal outcome
Women who do not receive regular mammograms are more likely than others to have breast cancer
diagnosed at an advanced stage
[…] thereby providing higher cytotoxicity against the 4T1 mouse mammary carcinoma cell line
All of this keywords are referred to the same biomedical concept, a search by breast cancer
will retrieve this three documents
‣ Use of context and semantic information to identify the relevant information
e.g. Search of CAT, that could be referred to the enzyme Catalase or to the animal, “cat”.
[..] activity of antioxidant enzymes (GSH-­Px, SOD, CAT) and content of malondialdehyde (MDA) were
determined
[…] 26 free-­living lynx, 53 domestic cats, 28 dogs, 33 red foxes (Vulpes vulpes) […]
The same keyword is referred to different biomedical concepts. Using the context, we can
identify that only the first sentence talks about an enzyme
by L cornide

26. Concept Relations
e.g. Search for Alzheimer’s Disease
The apolipoprotein E gene (APOE) polymorphism genotyping has an allegedly important predictive value
for coronary heart disorders and Alzheimer's disease.
Apolipoprotein E (apoE), a ligand for the low-­density lipoprotein receptor family, has been implicated in
modulating glial inflammatory responses and the risk of neurodegeneration associated with Alzheimer's
disease.
Although many genes have been suggested to be associated with AD, with the exception of APOE, most
polymorphic variants of potential risk exhibit a very weak association with AD
The protein apolipoprotein E and Alzheimer disease are related with a relevance of 36%
by L cornide

27. Knowledge Extraction
‣ Based on the detected relations between concepts, we can extract automatically
knowledge from text
e.g. Obtain the knowledge about Breast cancer, extracted from literature
[…] BRCA1 or BRCA2 […] Information was recorded on prophylactic mastectomy, prophylactic
oophorectomy, use of tamoxifen [..] had a bilateral prophylactic oophorectomy. […] breast cancer, 248
(18.0%) had had a prophylactic bilateral mastectomy. Among those who did not have a prophylactic
mastectomy, only 76 women (5.5%) took tamoxifen and 40 women (2.9%) took raloxifene for breast
cancer prevention. […].
Genes BRCA1 and BRCA2 are related with breast cancer. Tamoxifen and Raloxifene are drugs
used in its treatment, and mastectomy and oophorectomy are usual procedures to treat it.
by L cornide

28. Make new Discoveries
‣ Discover hidden relations between concepts that have not been described
before in the scientific literature
e.g. Obtain the knowledge about Breast cancer, extracted from literature
[…] meal fatty acids appear to be an important determinant of vascular reactivity, with fish oils
significantly improving postprandial endothelium-­independent vasodilation
Numerous studies have documented longer bleeding times and decreased platelet aggregation in
subjects ingesting omega-­3 fatty acids
vasomotor pain, in particular the fact of reactional vasodilation during Raynaud's syndrome,
inflammation in the region surrounding zones of ischemic necrosis, and infection of ulcers
Objective judgement on effects of medicine in patients with Raynaud's phenomenon-­-­measurement of
cutaneous blood flow using laser Doppler flowmeter and platelet aggregation activity
By finding evidence of a relation between fish oils and vasodilatation and platelet aggregation,
and evidence in the link between these two functions and Raynaud’s syndrome, we can uncover
a new discovery that was not described previously in the literature, the possible treatment of
Raynaud’s Syndrome with fish oil.
by L cornide

37. El Futuro
‣ Información estructurada.
‣ Identificador de usuario.
‣ El artículo del futuro.
‣ Búsqueda social.

38. http://beta.cell.com/erickson/

39. Collective
Social Search
Collaborative
Q&A
Friend-­Filtered
http://www.readwriteweb.com/archives/3_flavors_of_social_search_what_to_expect.php

40. Beta testers
Colaboración en el desarrollo de uno de los
principales buscadores biomédicos en el mercado.
Acceso a los últimas actualizaciones de nuestro
buscador.
Regalo seguro.
www.novoseek.com/betatesters.html

41. Contacto
Ramón Alonso-­Allende
Marketing & Business Development
allende@bioalma.com
Phone: +34 91 141 71 50