Bioinformatics and cancer research: building bridges for translational research

Genome studies have revolutionised cancer research in recent years as high-throughput technologies can now be used to identify sets of genes potentially related with different processes in cancer. However, managing all this data and organising it into useful datasets is still a challenge in the bioinformatics field. Finding relationships between the molecular and genomic information and the clinical information available, within the medical informatics domain, is currently driving the development of translational research in biomedicine. The dispersion and complexity of the molecular information, the poor adherence to standards, together with the fast evolution of the experimental techniques, pose obvious challenges for the development of integrated molecular resources. In parallel, restricted access to medical information together with the gaps in the development of standard terminologies are typical limitations in the area of medical informatics. The development of research projects combining medical and molecular information together with the current efforts to standardise and integrate databases and terminologies are described in this review as a demonstration of the fruitful activity in this area.

[1]  Lawrence Hunter,et al.  Enrichment of OBO ontologies , 2007, J. Biomed. Informatics.

[2]  Alfonso Valencia,et al.  Overview of BioCreAtIvE: critical assessment of information extraction for biology , 2005, BMC Bioinformatics.

[3]  Daniel L. Rubin,et al.  Using ontologies linked with geometric models to reason about penetrating injuries , 2006, Artif. Intell. Medicine.

[4]  Richard Baldock,et al.  An ontology of human developmental anatomy , 2003, Journal of anatomy.

[5]  V Maojo,et al.  Using Web Services for Linking Genomic Data to Medical Information Systems , 2007, Methods of Information in Medicine.

[6]  A. Valencia,et al.  Text-mining and information-retrieval services for molecular biology , 2005, Genome Biology.

[7]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[8]  Peter Woollard,et al.  The minimum information required for reporting a molecular interaction experiment (MIMIx) , 2007, Nature Biotechnology.

[9]  H. Garner.  Engineering in genomics: the emerging in-silico scientist; how text-based bioinformatics is bridging biology and artificial intelligence , 2004, IEEE Engineering in Medicine and Biology Magazine.

[10]  David Bryant,et al.  DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007, Nucleic Acids Res..

[11]  M. Olivier.  A haplotype map of the human genome , 2003, Nature.

[12]  Joaquín Dopazo,et al.  The role of the environment in Parkinson's disease. , 1996, Nucleic Acids Res..

[13]  Yugyung Lee,et al.  Ontology integration: Experience with medical terminologies , 2006, Comput. Biol. Medicine.

[14]  J J Cimino,et al.  The Practical Impact of Ontologies on Biomedical Informatics , 2006, Yearbook of Medical Informatics.

[15]  Robert Hoehndorf,et al.  Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies , 2007, BMC Bioinformatics.

[16]  V. Velculescu,et al.  Mutational analysis of gene families in human cancer. , 2005, Current opinion in genetics & development.

[17]  Alfonso Valencia,et al.  Automatic ontology construction from the literature. , 2002, Genome informatics. International Conference on Genome Informatics.

[18]  David Martin,et al.  Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network , 2003, Genome Biology.

[19]  Miguel García-Remesal,et al.  ONTOFUSION: Ontology-based integration of genomic and clinical databases , 2006, Comput. Biol. Medicine.

[20]  Michael Y. Galperin.  The Molecular Biology Database Collection: 2005 update , 2004, Nucleic Acids Res..

[21]  F. Mitelman,et al.  Recurrent chromosome aberrations in cancer. , 2000, Mutation research.

[22]  Tao Cai,et al.  Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary , 2005, Bioinform..

[23]  Francis S. Collins,et al.  Mapping the cancer genome , 2007 .

[24]  Jean Charlet,et al.  Building medical ontologies by terminology extraction from texts: An experiment for the intensive care units , 2006, Comput. Biol. Medicine.

[25]  T. Beißbarth,et al.  Interpreting experimental results using gene ontologies. , 2006, Methods in enzymology.

[26]  Franz Baader,et al.  SNOMED CT's Problem List: Ontologists' and Logicians' Therapy Suggestions , 2007, MedInfo.

[27]  Jean Charlet,et al.  Building an ontology of pulmonary diseases with natural language processing tools using textual corpora , 2007, Int. J. Medical Informatics.

[28]  Russ B. Altman,et al.  Application of Information Technology: A Statistical Approach to Scanning the Biomedical Literature for Pharmacogenetics Knowledge , 2004, J. Am. Medical Informatics Assoc..

[29]  K. Kinzler,et al.  Cancer genes and the pathways they control , 2004, Nature Medicine.

[30]  B. A. Ballif,et al.  ATM and ATR Substrate Analysis Reveals Extensive Protein Networks Responsive to DNA Damage , 2007, Science.

[31]  Alfonso Valencia,et al.  iHOP web services , 2007, Nucleic Acids Res..

[32]  Alfonso Valencia,et al.  Evaluation of BioCreAtIvE assessment of task 2 , 2005, BMC Bioinformatics.

[33]  Alexander A. Morgan,et al.  Gene name identification and normalization using a model organism database , 2004, J. Biomed. Informatics.

[34]  D. Zimonjic,et al.  Chromosome and gene alterations in breast cancer as markers for diagnosis and prognosis as well as pathogenetic targets for therapy. , 2002, American journal of medical genetics.

[35]  Francis S Collins,et al.  Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies. , 2007, Scientific American.

[36]  Dan Wu,et al.  EMBL Nucleotide Sequence Database in 2006 , 2006, Nucleic Acids Res..

[37]  A. Valencia,et al.  A gene network for navigating the literature , 2004, Nature Genetics.

[38]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[39]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[40]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[41]  Dong Xu,et al.  Global protein function annotation through mining genome-scale data in yeast Saccharomyces cerevisiae. , 2004, Nucleic acids research.

[42]  Alexander A. Morgan,et al.  Overview of BioCreAtIvE task 1B: normalized gene lists , 2005, BMC Bioinformatics.

[43]  B. Giusti,et al.  A model of anti-angiogenesis: differential transcriptosome profiling of microvascular endothelial cells from diffuse systemic sclerosis patients , 2006, Arthritis research & therapy.

[44]  Anand Kumar,et al.  Text mining and ontologies in biomedicine: Making sense of raw text , 2005, Briefings Bioinform..

[45]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[46]  T. Speed,et al.  GOstat: find statistically overrepresented Gene Ontologies within a group of genes. , 2004, Bioinformatics.

[47]  Purvesh Khatri,et al.  Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate , 2003, Nucleic Acids Res..

[48]  Dennis B. Troup,et al.  NCBI GEO: mining tens of millions of expression profiles—database and tools update , 2006, Nucleic Acids Res..

[49]  Robert Meersman,et al.  On the Move to Meaningful Internet Systems 2004: CoopIS, DOA, and ODBASE , 2004, Lecture Notes in Computer Science.

[50]  Hongfang Liu,et al.  Gene name ambiguity of eukaryotic nomenclatures , 2005, Bioinform..

[51]  Chris Sander,et al.  CancerGenes: a gene selection resource for cancer genome projects , 2006, Nucleic Acids Res..

[52]  Alfonso Valencia,et al.  CARGO: a web portal to integrate customized biological information , 2007, Nucleic Acids Res..

[53]  H. Mages,et al.  Cloning of ATAC, an activation‐induced, chemokine‐related molecule exclusively expressed in CD8+ T lymphocytes , 1995, European journal of immunology.

[54]  Alfonso Valencia,et al.  Text-mining approaches in molecular biology and biomedicine. , 2005, Drug discovery today.

[55]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[56]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[57]  Lipika Dey,et al.  Biological ontology enhancement with fuzzy relations: a text-mining framework , 2005, The 2005 IEEE/WIC/ACM International Conference on Web Intelligence (WI'05).

[58]  Olivier Bodenreider,et al.  The Unified Medical Language System (UMLS): integrating biomedical terminology , 2004, Nucleic Acids Res..

[59]  Michael Y. Galperin.  The Molecular Biology Database Collection: 2007 update , 2006, Nucleic Acids Res..

[60]  Russ B Altman,et al.  Extracting and characterizing gene-drug relationships from the literature. , 2004, Pharmacogenetics.

[61]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[62]  Ioannis G. Tollis,et al.  SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics – exploring current scientific literature for emerging topics , 2007, BMC Bioinformatics.

[63]  C. McDonald,et al.  LOINC, a universal standard for identifying laboratory observations: a 5-year update. , 2003, Clinical chemistry.

[64]  Alfonso Valencia,et al.  Implementing the iHOP concept for navigation of biomedical literature , 2005, ECCB/JBI.

[65]  V Maojo,et al.  Designing New Methodologies for Integrating Biomedical Information in Clinical Trials , 2006, Methods of Information in Medicine.

[66]  Alfonso Valencia.  Bioinformatics: Biology by other means , 2002, Bioinform..

[67]  T. Schall,et al.  Molecular cloning and functional characterization of human lymphotactin. , 1995, Journal of immunology.

[68]  Elena Beisswanger,et al.  Towards a Top-Domain Ontology for Linking Biomedical Ontologies , 2007, MedInfo.

[69]  Daniel L. Rubin,et al.  Ontology-based Annotation and Query of Tissue Microarray Data , 2006, AMIA.

[70]  Sergio Storari,et al.  Finding biological process modifications in cancer tissues by mining gene expression correlations , 2005, BMC Bioinformatics.

[71]  O. Yoshie,et al.  Molecular cloning of a novel C or γ type chemokine, SCM‐1 , 1995 .

[72]  Stanley Letovsky,et al.  Predicting protein function from protein/protein interaction data: a probabilistic approach , 2003, ISMB.

[73]  Steffen Staab,et al.  Learning Concept Hierarchies from Text Corpora using Formal Concept Analysis , 2005, J. Artif. Intell. Res..

[74]  Evelyn Camon,et al.  The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..

[75]  Walter Daelemans,et al.  Automatic Initiation of an Ontology , 2004, CoopIS/DOA/ODBASE.

[76]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[77]  Paolo Terenziani,et al.  Towards a Flexible Integration of Clinical Guideline Systems with Medical Ontologies and Medical Information Systems , 2004, CGP.

[78]  May D. Wang,et al.  GoMiner: a resource for biological interpretation of genomic and proteomic data , 2003, Genome Biology.

[79]  Debnath Pal,et al.  On gene ontology and function annotation , 2006, Bioinformation.

[80]  Carole A. Goble,et al.  Ontology-based Knowledge Representation for Bioinformatics , 2000, Briefings Bioinform..

[81]  Jean Charlet,et al.  Methodology to Build Medical Ontology from Textual Resources , 2006, AMIA.

[82]  Christian Blaschke,et al.  Text Mining for Metabolic Pathways, Signaling Cascades, and Protein Networks , 2005, Science's STKE.

[83]  Anita Burgun-Parenthoine,et al.  Integrating Biological Pathways in Disease Ontologies , 2007, MedInfo.

[84]  A. Valencia,et al.  The success (or not) of HUGO nomenclature , 2006, Genome Biology.

[85]  Russ B. Altman.  Viewpoint: The Interactions Between Clinical Informatics and Bioinformatics: A Case Study , 2000, J. Am. Medical Informatics Assoc..

[86]  H. Herzel,et al.  Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases , 2006 .