Science Bioinformatics Data Resources

8/12/2019 Science Bioinformatics Data Resources

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June 10/11, 2014

Michelle Hudson, Science & Social Science Data LibrarianKristin Bogdan , Science & Social Science Data Librarian

Kayleigh Bohmier, Science Research Support Librarian for Astronomy,

Geology & Geophysics, and Physics

Rolando Garcia-Milian, Biomedical Sciences Research Support

Science Data Resources: From Astronomy to Bioinformatics


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A Brief Overview of Data in theSciences


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Examples of data

questions

Where would you find

these? Spectroscopy on jars found

in wrecks Spectra of M31 ApoE structure Ice cores Genomic sequences for

extinct mammals


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Types of Data Observational

data captured in real time, irreplaceable sensor readings, telescope images, geologic samples

Experimental data from lab equipment, expensive to reproduce gene sequences

Simulation data generated from models (models are more important than the

data) Derived or compiled

data put together from other information 3D models, compileddatabases


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Formats of data Documents, spreadsheets, lab notebooks, questionnaires, survey

responses, health indicators, audio recordings, video recordings,

protein and gene sequences, images, films, spectra, slides,

artifacts, specimens, samples, models, algorithms, scripts,

software code, etc.


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General resources data.gov: http://www.data.gov/ DataONE: http://www.dataone.org/ NCBI: http://www.ncbi.nlm.nih.gov/ EBI: http://www.ebi.ac.uk/ FigShare: http://figshare.com/ Dryad: http://datadryad.org/ PLOS|ONE: http://www.plosone.org/

Data journals:http://mlibrarydata.wordpress.com/2014/05/09/data-journals/

Research guide: http://guides.library.yale.edu/sciencedata
http://mlibrarydata.wordpress.com/2014/05/09/data-journals/http://guides.library.yale.edu/sciencedatahttp://guides.library.yale.edu/sciencedatahttp://guides.library.yale.edu/sciencedatahttp://guides.library.yale.edu/sciencedatahttp://guides.library.yale.edu/sciencedatahttp://mlibrarydata.wordpress.com/2014/05/09/data-journals/http://mlibrarydata.wordpress.com/2014/05/09/data-journals/http://mlibrarydata.wordpress.com/2014/05/09/data-journals/http://mlibrarydata.wordpress.com/2014/05/09/data-journals/


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Astronomy,or,

Massively Open Online Archives


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Astronomy data Self-collected Data.NASA.gov US Virtual Observatory

(US VO) ApJ supplement Research centers and

collaborations

Figshare Astronomy Dataverse github

Screenshot: Virtual Observatory Data Explorer search for M31


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Government Data NASA Data processing levels

Ranked 0-4 Level 0 is raw data Level 1 has been

processed and error-corrected

This is, incidentally, where conspiracy theoriescome from

Level 2 data maycontain derivedparameters

Levels 3+ have furtherprocessing
http://data.nasa.gov/http://archive.eso.org/cms.htmlhttp://vao.stsci.edu/portal/Mashup/Clients/Portal/DataDiscovery.htmlhttp://archive.stsci.edu/


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Data fromResearchers

Astrophysical Journal

Supplement http://dx.doi.org/10.1088/00

67-0049/212/2/26 http://dx.doi.org/10.1088/00

67-0049/212/2/19 http://dx.doi.org/10.1088/00

67-0049/212/1/6 Project web pages (i.e.,

Kepler) Intermediary data products

remain a problem (i.e., code,

analyzed data sets)

Olausen, S. A., & Kaspi, V. M. (2014). Table 2 from TheMcGill Magnetar Catalog. The Astrophysical Journal Supplement Series, 212 (1), 1-22. doi:10.1088/0067-0049/212/1/6
http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/1/6http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/19http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26http://dx.doi.org/10.1088/0067-0049/212/2/26


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Harvards Astronomy Dataverse A solution for intermediate stage data products


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Physics:

A Little Less Open,But Everyone Knows Where To Find It


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Reference Data National Nuclear Data

Center at Brookhaven

National Laboratory:

http://www.nndc.bnl.gov/ Department of Energy Data

Explorer:

http://www.osti.gov/dataexp

lorer/ MCPlots (Monte Carlo plots

reference for HEP):

http://mcplots.cern.ch/

Monte Carlo plot reference from MCPlots
http://www.nndc.bnl.gov/http://www.osti.gov/dataexplorer/http://www.osti.gov/dataexplorer/http://mcplots.cern.ch/http://mcplots.cern.ch/http://mcplots.cern.ch/http://www.osti.gov/dataexplorer/http://www.osti.gov/dataexplorer/http://www.osti.gov/dataexplorer/http://www.nndc.bnl.gov/http://www.nndc.bnl.gov/


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Experimental Data Durham HepData Project

Reactions database Data from active

experiments

Data reviews http://durpdg.dur.ac.uk/H

EPDATA/REAC Example:

http://durpdg.dur.ac.uk/view/ins1297226

Experimental data releases IceCube:

http://icecube.wisc.edu/science/data
http://durpdg.dur.ac.uk/HEPDATA/REAChttp://durpdg.dur.ac.uk/HEPDATA/REAChttp://durpdg.dur.ac.uk/view/ins1297226http://durpdg.dur.ac.uk/view/ins1297226http://icecube.wisc.edu/science/datahttp://icecube.wisc.edu/science/datahttp://icecube.wisc.edu/science/datahttp://icecube.wisc.edu/science/datahttp://icecube.wisc.edu/science/datahttp://durpdg.dur.ac.uk/view/ins1297226http://durpdg.dur.ac.uk/view/ins1297226http://durpdg.dur.ac.uk/view/ins1297226http://durpdg.dur.ac.uk/HEPDATA/REAChttp://durpdg.dur.ac.uk/HEPDATA/REAChttp://durpdg.dur.ac.uk/HEPDATA/REAC


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and then, we have the data grids.


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Geoscience Data Resources


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Kinds of

Geoscience Data Geospatial Rocks and Minerals Economic Geology Paleobiology Climate History Geochemistry Physical Samples

Image credit: USGS, via Wikimedia Commons:http://commons.wikimedia.org/wiki/File:Seismograph_Pinat ubo.jpg


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Physical Samples

as Data Identified as data in NSF

guidelines Different analyses = new

data New techniques

developed over time Repositories for samples

specific metadata

requiredGry, Parent. 7 May 2011. Peronopsis interstrictus. Retrieved

from the Wikimedia Commons athttp://commons.wikimedia.org/wiki/File%3APeronopsis_interstrictus_White%2C_1874_2.jpg


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Geo/Paleo Sample Repositories/Registries International Geo Sample Number (IGSN) -

http://www.geosamples.org/ Peabody Museum - http://peabody.yale.edu/collections/search-

collections PaleoBioDB - http://paleobiodb.org/#/
http://www.geosamples.org/http://peabody.yale.edu/collections/search-collectionshttp://peabody.yale.edu/collections/search-collectionshttp://paleobiodb.org/http://paleobiodb.org/http://paleobiodb.org/http://peabody.yale.edu/collections/search-collectionshttp://peabody.yale.edu/collections/search-collectionshttp://peabody.yale.edu/collections/search-collectionshttp://peabody.yale.edu/collections/search-collectionshttp://www.geosamples.org/http://www.geosamples.org/


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Other Resources for Geoscience USGS Earth Explorer - http://earthexplorer.usgs.gov/ Data.Gov - http://www.data.gov/ GeoGratis - http://geogratis.cgdi.gc.ca/ Morphobank - http://morphobank.org/ EarthCube http://earthcube.org/ CINERGI - http://workspace.earthcube.org/cinergi
http://earthexplorer.usgs.gov/http://geogratis.cgdi.gc.ca/http://morphobank.org/http://earthcube.org/http://workspace.earthcube.org/cinergihttp://workspace.earthcube.org/cinergihttp://workspace.earthcube.org/cinergihttp://earthcube.org/http://earthcube.org/http://morphobank.org/http://morphobank.org/http://geogratis.cgdi.gc.ca/http://geogratis.cgdi.gc.ca/http://earthexplorer.usgs.gov/http://earthexplorer.usgs.gov/


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Problem Rapid Growth of Biomedical data

GenBank Statistics http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/

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2000 2001 20022003 20042005 200620072008 2009 2010 2011 2012

M i l l i o n s

Samples Submitted to Gene ExpressionOmnibus Database

Compiled from GEO historic datahttp://www.ncbi.nlm.nih.gov/geo/summary/?type=history
http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/http://www.ncbi.nlm.nih.gov/geo/summary/?type=historyhttp://www.ncbi.nlm.nih.gov/geo/summary/?type=historyhttp://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/http://www.ncbi.nlm.nih.gov/genbank/genbankstats-2008/


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Compiled by from PubMedhttp://www.ncbi.nlm.nih.gov/pubmed

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1940 1960 1980 2000 2020

M i l l i o n s

Number of Records in PubMed

Biomedical Literature

Problem Growth of the Biomedical Literature

Huge volume (PubMed 23132342citations)

High diversity

High quality (peer review)

Users overwhelmed by long list of search results

1/3 of Pubmed queries result in 100 or more citations (Islamaj,2009)
http://www.ncbi.nlm.nih.gov/pubmedhttp://www.ncbi.nlm.nih.gov/pubmed


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Querying the biomedical literature becomes more difficult

Medical Subject HeadingsFiltersBoolean operators

Problem Querying the Biomedical Literature


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Modified from OpenHelix

EGFR

retrieves documents/ records

T14D inh ibi ted EGF receptor internal izat ion

EGFR regulates tum or cel l pro l i ferat ion

EGFR is express ed in SCCHN

extracts facts

Information Retrieval

records

Information Extraction

records

Information Retrieval vs Information Extraction


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Alternative Tools for Mining the Biomedical Literature

Alternative tools for mining the biomedical literature combine:

Statistical methods,

Ontologies / Controlled vocabularies

Natural Language Processing tools,

Visualization tools

Reduced time for discovering meaningfulresults.


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Alternative Mining Tools for the Biomedical Literature


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Main gene query

Protein/gene associated

Synonym

Medical terminology (MeSH)


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Linked to Entrez Geneand OMIM database


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Workshop- Novel Online Tools for Mining the BiomedicalLiterature


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Case 1 Few Results in the Biomedical Literature

Searching for novel genes


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Searching for side effects of drugs: Cerebyx respiratory failure


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Phenotypic information can be usedto infer molecular interactions andhinting at new uses of marketeddrugs (Campillos, 2008)



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Data Annotation/ Integration / Visualization Tools GenomeBrowsers


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Workshop- Novel Online Tools for Mining the BiomedicalLiterature


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Contextualizing Data/Results in the Biomedical Knowledge

Resulting list of upregulated genes aftertreatment of prostatecancer cells with VitD

Microarray dataobtained from GeneExpression Omnibusrepository wasanalyzed withGEO2R statisticalsoftware


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Contextualizing Data/Results in the Biomedical Knowledge


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References

Campillos M*, Kuhn M*, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-

effect similarity. Science. 2008 Jul 11;321(5886):263-6.http://www.ncbi.nlm.nih.gov/pubmed/18621671

Islamaj Dogan R, Murray GC, Nvol A, Lu Z. (2009) Understanding PubMed user search behavior. Database (Oxford) http://www.ncbi.nlm.nih.gov/pubmed/20157491

Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The humangenome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.http://www.ncbi.nlm.nih.gov/pubmed/12045153

Kuhn M, Campillos M, Letunic I, Jensen LJ, Bork P. A side effect resource to capturephenotypic effects of drugs. Mol Syst Biol. 2010;6:343. Epub 2010 Jan 19.http://sideeffects.embl.de/drugs/56338/

Rindflesch, T.C. et al. (2011) Semantic MEDLINE: An advanced information management

application for biomedicine. Information Services & Use, 31, 15-21.http://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdf
http://www.ncbi.nlm.nih.gov/pubmed/18621671http://www.ncbi.nlm.nih.gov/pubmed/20157491http://www.ncbi.nlm.nih.gov/pubmed/12045153http://sideeffects.embl.de/drugs/56338/http://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://lhncbc.nlm.nih.gov/system/files/pub-lhncbc-2011-109.pdfhttp://sideeffects.embl.de/drugs/56338/http://www.ncbi.nlm.nih.gov/pubmed/12045153http://www.ncbi.nlm.nih.gov/pubmed/20157491http://www.ncbi.nlm.nih.gov/pubmed/20157491http://www.ncbi.nlm.nih.gov/pubmed/18621671


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Science Bioinformatics Data Resources

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