Informatic system for a global tissue–fluid biorepository with a graph theory–oriented graphical user interface

References

• Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, Jouvet A et al. The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007; 114: 97–109.
   PubMed Web of Science ®Google Scholar
• Sathornsumetee S, Rich JN, Reardon DA. Diagnosis and treatment of high-grade astrocytoma. Neurol Clin. 2007; 25: 1111–39. x.
   PubMed Web of Science ®Google Scholar
• Mellinghoff IK, Wang MY, Vivanco I, Haas-Kogan DA, Zhu S, Dia EQ et al. Molecular determinants of the response of glioblastomas to EGFR kinase inhibitors. N Engl J Med. 2005; 353: 2012–24.
   PubMed Web of Science ®Google Scholar
• Baldewpersad Tewarie NM, Burgers IA, Dawood Y, den Boon HC, den Brok MG, Klunder JH et al. NADP+ -dependent IDH1 R132 mutation and its relevance for glioma patient survival. Med Hypotheses. 2013; 80: 728–31.
   Web of Science ®Google Scholar
• Aronson JK. Biomarkers and surrogate endpoints. Br J Clin Pharmacol. 2005; 59: 491–4.
   PubMed Web of Science ®Google Scholar
• Prentice RL. Surrogate and mediating endpoints: current status and future directions. J Natl Cancer Inst. 2009; 101: 216–17.
   PubMed Web of Science ®Google Scholar
• Amin W, Parwani AV, Schmandt L, Mohanty SK, Farhat G, Pople AK et al. National Mesothelioma Virtual Bank: a standard based biospecimen and clinical data resource to enhance translational research. BMC cancer. 2008; 8: 236.
   Web of Science ®Google Scholar
• BioServe – Molecular Services. Human DNA, RNA, Serum and Tissue Bank. Repository Network. [cited 2014 May 30]. Available from: http://www.bioserve.com/.
   Google Scholar
• Home Page – Biorepositories and Biospecimen Research Branch. [cited 2014 May 30]. Available from: http://biospecimens.cancer.gov/default.asp.
   Google Scholar
• Google Apps for Business. Google, Inc. 2014. [cited 2014 August 15]. Available from: http://www.google.com/intl/en/enterprise/apps/business/.
   Google Scholar
• Kalra H, Simpson RJ, Ji H, Aikawa E, Altevogt P, Askenase P et al. Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PLoS Biol. 2012; 10: e1001450.
   PubMed Web of Science ®Google Scholar
• Kim DK, Kang B, Kim OY, Choi DS, Lee J, Kim SR et al. EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles. J Extracell Vesicles. 2013; 2 20384.
   Google Scholar
• Mathivanan S, Fahner CJ, Reid GE, Simpson RJ. ExoCarta 2012: database of exosomal proteins, RNA and lipids. Nucleic Acids Res. 2014; 40: D1241–4.
   Web of Science ®Google Scholar
• US National Center for Bio Medical Ontology (NCBO). 2014. [cited 2014 May 30]. Available from: http://www.bioontology.org/.
   Google Scholar
• Sintupisut N, Liu PL, Yeang CH. An integrative characterization of recurrent molecular aberrations in glioblastoma genomes. Nucleic Acids Res. 2013; 41: 8803–21.
   Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008; 455: 1061–8.
   PubMed Web of Science ®Google Scholar
• Rohn H, Junker A, Hartmann A, Grafahrend-Belau E, Treutler H, Klapperstuck M et al. VANTED v2: a framework for systems biology applications. BMC Syst Biol. 2012; 6: 139.
   Web of Science ®Google Scholar
• Rohn H, Klukas C, Schreiber F. Creating views on integrated multidomain data. Bioinformatics. 2011; 27: 1839–45.
   Web of Science ®Google Scholar
• Pavlopoulos GA, Secrier M, Moschopoulos CN, Soldatos TG, Kossida S, Aerts J et al. Using graph theory to analyze biological networks. BioData Min. 2011; 4: 10.
   PubMed Web of Science ®Google Scholar
• Chao SY. Graph theory and analysis of biological data in computational biology. InTech. 2009. [cited 2014 May 30]. Available from: http://www.intechopen.com/books/advanced-technologies/graph-theory-and-analysis-of-biological-data-in-computational-biology.
   Google Scholar
• Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G et al. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014; 42: D472–7.
   PubMed Web of Science ®Google Scholar
• Kumar A, Suthers PF, Maranas CD. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinformatics. 2012; 13: 6.
   Web of Science ®Google Scholar
• Sowa JF. Conceptual structures: information processing in mind and machine. 1984; Reading, MA: Addison-Wesley. The Systems programming series.
   Google Scholar
• Filipe V, Hawe A, Jiskoot W. Critical evaluation of Nanoparticle Tracking Analysis (NTA) by NanoSight for the measurement of nanoparticles and protein aggregates. Pharm Res. 2010; 27: 796–810.
   PubMed Web of Science ®Google Scholar
• Momen-Heravi F, Balaj L, Alian S, Mantel PY, Halleck AE, Trachtenberg AJ et al. Current methods for the isolation of extracellular vesicles. Biol Chem. 2013; 394: 1253–62.
   PubMed Web of Science ®Google Scholar
• Momen-Heravi F, Balaj L, Alian S, Tigges J, Toxavidis V, Ericsson M et al. Alternative methods for characterization of extracellular vesicles. Front Physiol. 2012; 3: 354.
   PubMed Web of Science ®Google Scholar
• Belmonte NG. JavaScript InfoVis Toolkit ver. 2.01. 2013. [cited 2014 May 30]. Available from: http://philogb.github.com/jit/.
   Google Scholar
• Biorepository Accreditation Program Standards for Accreditation. College of American Pathologists. 2013. [cited 2014 May 30]. Available from: http://www.cap.org/apps/docs/laboratory_accreditation/build/pdf/bap_standards.pdf.
   Google Scholar
• Witwer KW, Buzas EI, Bemis LT, Bora A, Lasser C, Lotvall J et al. Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. J Extracell Vesicles. 2013; 2 20360.
   PubMedGoogle Scholar
• Brandes AA, Tosoni A, Spagnolli F, Frezza G, Leonardi M, Calbucci F et al. Disease progression or pseudoprogression after concomitant radiochemotherapy treatment: pitfalls in neurooncology. Neuro Oncol. 2008; 10: 361–7.
   PubMed Web of Science ®Google Scholar
• Oracle. Oracle Java ver. 1.7.x. Oracle Corporation. 2014. [cited 2014 May 30]. Available from: http://www.java.com.
   Google Scholar
• PostgreSQL Global Development Group. PostgreSQL ver. 9.2.x. 2014. [cited 2014 May 30]. Available from: http://www.postgresql.org/.
   Google Scholar
• Odersky M. Scala ver. 2.10.x. École Polytechnique Fédérale de Lausanne (EPFL). 2014. [cited 2014 May 30]. Available from: http://www.scala-lang.org/.
   Google Scholar
• Odersky M. The Interactive Interpreter (REPL) Scala ver. 2.10.x. École Polytechnique Fédérale de Lausanne (EPFL). 2014. [cited 2014 May 30]. Available from: http://www.scala-lang.org/node/2097.
   Google Scholar
• Apple. WebObjects ver 5.4.3. Apple, Inc. 2008. [cited 2014 August 15]. Available from: https://www.apple.com/support/webobjects/.
   Google Scholar
• Apple. Enterprise Objects Framework (EOF). 2007. [cited 2014 August 15]. Available from: http://developer.apple.com/legacy/mac/library/documentation/WebObjects/Enterprise_Objects/EnterpriseObjects.pdf.
   Google Scholar
• Gurley R, Robert P. The D2W rule system. [cited 2014 August 15]. Available from: http://wiki.wocommunity.org/display/documentation/The+D2W+Rule+System.
   Google Scholar
• Foundation j. jQuery ver. 1.9.x. jQuery Foundation. 2014. [cited 2014 August 15]. Available from: http://jquery.com/.
   Google Scholar
• NCBO Widgets. Term-selection field on a form. U.S. National Center for Bio Medical Ontology. 2014. [cited 2014 August 15]. Available from: http://www.bioontology.org/wiki/index.php/NCBO_Widgets#Term-selection_field_on_a_form.
   Google Scholar
• Liferay ver. 6.x. Liferay, Inc. 2014. [cited 2014 August 15]. Available from: http://www.liferay.com.
   Google Scholar
• JSR 286: Portlet Specification. Oracle Corporation. 2013. [cited 2014 August 15]. Available from: https://jcp.org/aboutJava/communityprocess/final/jsr286/.
   Google Scholar
• OpenSocial ver. 2.x. OpenSocial Foundation. 2014. [cited 2014 August 15]. Available from: http://docs.org/display/OS/Home.
   Google Scholar
• Google Maps API ver. 3.x. Google, Inc. 2014. [cited 2014 August 15]. Available from: https://developers.google.com/maps/.
   Google Scholar
• SNOMED Clinical Terms® (SNOMED CT®) [Product, program, and project descriptions]. [cited 2014 August 15]. Available from: http://www.nlm.nih.gov/research/umls/Snomed/snomed_main.html.
   Google Scholar
• UMLS Terminology Services – License. [cited 2014 August 15]. Available from: https://uts.nlm.nih.gov/license.html.
   Google Scholar
• The CentOs Project. CentOS-5 documentation. [cited 2014 August 15]. Available from: http://www.centos.org/docs/5/.
   Google Scholar
• bio4j ver. 0.9. 2014. [cited 2014 August 15]. Available from: http://bio4j.com.
   Google Scholar
• Amazon Web Services. Amazon Elastic Compute Cloud (EC2) – Scalable Cloud Servers. [cited 2014 August 15]. Available from: http://aws.amazon.com/ec2/.
   Google Scholar
• OAuth. 2014. [cited 2014 August 15]. Available from: http://oauth.net.
   Google Scholar
• Apps Script. Google, Inc. 2014. [cited 2014 August 15]. Available from: http://developers.google.com/apps-script/.
   Google Scholar
• NCI Metathesaurus. vol. 2.3. 2014; U.S. National Cancer Institute. [cited 2014 August 15]. Available from: http://ncimeta.nci.nih.gov/ncimbrowser/.
   Google Scholar
• Summary of the HIPAA privacy rule. U.S. Department of Health & Human Services. 2014. [cited 2014 August 15]. Available from: http://www.hhs.gov/ocr/privacy/hipaa/understanding/summary/index.html.
   Google Scholar
• U.S. Department of Health & Human Services. HIPAA administrative simplification statute and rules – security rule. 2014. [cited 2014 August 15]. Available from: http://www.hhs.gov/ocr/privacy/hipaa/administrative/securityrule/securityruleguidance.html.
   Google Scholar
• Office of the Commissioner, U S Food and Drug Administration. Guidance for industry. Computerized systems used in clinical investigations. 2007; U.S. Department of Health and Human Services. [cited 2014 August 15]. Available from: http://www.fda.gov/downloads/Drugs/GuidanceComplianceRegulatoryInformation/Guidances/UCM070266.pdf.
   Google Scholar
• WMA declaration of Helsinki – ethical principles for medical research involving human subjects. [cited 2014 August 15]. Available from: http://www.wma.net/en/30publications/10policies/b3/.
   Google Scholar
• WMA declaration on ethical considerations regarding health databases. [cited 2014 August 15]. Available from: http://www.wma.net/en/30publications/10policies/d1/.
   Google Scholar
• Medical privacy in principle. Privacy International. [cited 2014 August 15]. Available from: https://www.privacyinternational.org/reports/privacy-and-security-in-developing-countries-and-emergency-sitmedical-privacy-in
   Google Scholar
• Security-Enhanced Linux (SELINUX). U.S. National Security Agency, Central Security Service. 2009. [cited 2014 August 15]. Available from: http://www.nsa.gov/research/selinux/.
   Google Scholar
• Tomcat ver. 6.x. The Apache Software Foundation. 2013. [cited 2014 August 15]. Available from: http://tomcat.apache.org/.
   Google Scholar
• The Apache Software Foundation. 2014. httpd 2.x. [cited 2014 August 15]. Available from: http://www.apache.org.
   Google Scholar
• Rosse C, Mejino JL Jr. A reference ontology for biomedical informatics: the Foundational Model of Anatomy. J Biomed Inform. 2003; 36: 478–500.
   PubMed Web of Science ®Google Scholar
• Nichols BN, Mejino JL, Detwiler LT, Nilsen TT, Martone ME, Turner JA et al. Neuroanatomical domain of the foundational model of anatomy ontology. J Biomed Semantics. 2014; 5: 1.
   Web of Science ®Google Scholar
• SNOMED-CT Standard Nomenclature in Medicine Clinical Terms. International Health Terminology Standards Development Organisation. 2014. [cited 2014 August 15]. Available from: http://www.ihtsdo.org/snomed-ct/.
   Google Scholar
• North D. Behavior driven development. [cited 2014 August 15]. Available from: http://leanagilemachine.blogspot.com/p/bdd.html.
   Google Scholar
• Bostock M. Data driven documents D3.js. 2013. [cited 2014 August 15]. Available from: http://d3js.org/.
   Google Scholar
• Kao D. Code: gene ontology data visualization with D3.js and python. 2012. [cited 2014 August 15]. Available from: http://blog.nextgenetics.net/?e=19 vol. 2014.
   Google Scholar
• Vicknair C, Macias M, Zhendong Z, Nan Z, Chen Y, Wilkins D. A comparison of a graph database and a relational database: a data provenance perspective. The 48th ACM Southeast Conference. vol. 10. [cited 2014 May 30]. Available from: http://www.cs.olemiss.edu/ychen/publications/conference/vicknair_acmse10.pdf.
   Google Scholar
• Pareja P. Bio4j 0.9 the billion relationships are here!. vol. 2014. oh no sequences!. 2013. [cited 2014 May 30]. Available from: http://bio4j.com/blog/2013/10/bio4j-09-the-billion-relationships-is-here/.
   Google Scholar
• Cotter D, Maer A, Guda C, Saunders B, Subramaniam S. LMPD: LIPID MAPS proteome database. Nucleic Acids Res. 2006; 34: D507–10.
   Web of Science ®Google Scholar
• Spring ROO ver. 1.2.3. Spring Source, VMWare, Inc. 2012. [cited 2014 May 30]. Available from: http://www.springsource.org/spring-roo.
   Google Scholar
• Ruby on Rails ver. 4.0.x. 37 Signals. 2013. [cited 2014 May 30]. Available from: http://rubyonrails.org.
   Google Scholar
• GoPivotal. Grails 2.3.x. GoPivotal, Inc. 2014. [cited 2014 May 30]. Available from: http://grails.org.
   Google Scholar
• Federighi C, Ngan K. AribaWeb ver. 5.2. Ariba, Inc. 2013. [cited 2014 May 30]. Available from: http://aribaweb.org/.
   Google Scholar
• Mergen MF, Uhlig V, Krieger O, Xenidis J. Virtualization for high-performance computing. SIGOPS Oper Syst Rev. 2006; 40: 8–11.
   Google Scholar
• ISO 27001. International Standards Organization. 2014. [cited 2014 May 30]. Available from: http://27000.org/iso-27001.htm.
   Google Scholar
• AWS Security Center. Amazon Web Services. 2013. [cited 2014 May 30]. Available from: http://aws.amazon.com/security/.
   Google Scholar
• Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL et al. Open PHACTS: semantic interoperability for drug discovery. Drug Discov Today. 2012; 17: 1188–98.
   PubMed Web of Science ®Google Scholar
• RFA-RM-12-010. Data Management and Resource Repository (DMRR) on Extracellular RNA (U54). 2012. [cited 2014 May 30]. Available from: http://grants.nih.gov/grants/guide/rfa-files/RFA-RM-12-010.html.
   Google Scholar
• Choi DS, Kim DK, Kim YK, Gho YS. Proteomics of extracellular vesicles: exosomes and ectosomes. Mass Spectrom Rev. 2014
   Web of Science ®Google Scholar
• Mathivanan S, Ji H, Simpson RJ. Exosomes: extracellular organelles important in intercellular communication. J Proteomics. 2010; 73: 1907–20.
   PubMed Web of Science ®Google Scholar
• Chen H, Yu T, Chen JY. Semantic web meets integrative biology: a survey. Brief Bioinform. 2013; 14: 109–25.
   Web of Science ®Google Scholar