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Karatzas E, Zachariou M, Bourdakou MM, Minadakis G, Oulas A, Kolios G, Delis A, Spyrou GM. PathWalks: identifying pathway communities using a disease-related map of integrated information. Bioinformatics 2020; 36:4070-4079. [PMID: 32369599 PMCID: PMC7332569 DOI: 10.1093/bioinformatics/btaa291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 04/11/2020] [Accepted: 04/27/2020] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming and costly task. Computational methodologies that propose pathway/mechanism communities and reveal respective relationships can be of great value as they can help expedite the process of identifying how perturbations in a single pathway can affect other pathways. RESULTS We present a random-walks-based methodology called PathWalks, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study.We apply the PathWalks methodology on Alzheimer's disease and idiopathic pulmonary fibrosis and establish that it can highlight pathways that are also identified by other pathway analysis tools as well as are backed through bibliographic references. More importantly, PathWalks produces additional new pathways that are functionally connected with those already established, giving insight for further experimentation. AVAILABILITY AND IMPLEMENTATION https://github.com/vagkaratzas/PathWalks. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Evangelos Karatzas
- Department of Informatics and Telecommunications, University of Athens, Athens 15703, Greece
| | - Margarita Zachariou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Marilena M Bourdakou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,Department of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece
| | - George Minadakis
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Anastasis Oulas
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - George Kolios
- Department of Medicine, Laboratory of Pharmacology, Democritus University of Thrace, Komotini, Greece
| | - Alex Delis
- Department of Informatics and Telecommunications, University of Athens, Athens 15703, Greece
| | - George M Spyrou
- Department of Bioinformatics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus.,The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
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Triplet T, Shortridge MD, Griep MA, Stark JL, Powers R, Revesz P. PROFESS: a PROtein function, evolution, structure and sequence database. Database (Oxford) 2010; 2010:baq011. [PMID: 20624718 PMCID: PMC2911846 DOI: 10.1093/database/baq011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 06/03/2010] [Accepted: 06/06/2010] [Indexed: 11/13/2022]
Abstract
The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are approximately 1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein-protein interaction networks. Database URL: http://cse.unl.edu/~profess/
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Affiliation(s)
- Thomas Triplet
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Matthew D. Shortridge
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Mark A. Griep
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Jaime L. Stark
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Robert Powers
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
| | - Peter Revesz
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588-0115 and Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 68588-0304, USA
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3
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Go EP. Database Resources in Metabolomics: An Overview. J Neuroimmune Pharmacol 2009; 5:18-30. [DOI: 10.1007/s11481-009-9157-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 04/15/2009] [Indexed: 12/22/2022]
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Ganter B, Zidek N, Hewitt PR, Müller D, Vladimirova A. Pathway analysis tools and toxicogenomics reference databases for risk assessment. Pharmacogenomics 2008; 9:35-54. [PMID: 18154447 DOI: 10.2217/14622416.9.1.35] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The pharmaceutical industry has begun to leverage a range of new technologies (proteomics, pharmacogenomics, metabolomics and molecular toxicology [e.g., toxicogenomics]) and analysis tools that are becoming increasingly integrated in the area of drug discovery and development. The approach of analyzing the vast amount of toxicogenomics data generated using molecular pathway and networks analysis tools in combination with analysis of reference data will be the main focus of this review. We will demonstrate how this combined approach can increase the understanding of the molecular mechanisms that lead to chemical-induced toxicity and application of this knowledge to compound risk assessment. We will provide an example of the insights achieved through a molecular toxicology analysis based on the well-known hepatotoxicant lipopolysaccharide to illustrate the utility of these new tools in the analysis of complex data sets, both in vivo and in vitro. The ultimate objective is a better lead selection process that improves the chances for success across the different stages of drug discovery and development.
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Affiliation(s)
- Brigitte Ganter
- Ingenuity Systems, 1700 Seaport Blvd, Redwood City, CA 94063, USA.
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5
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Ekins S, Shimada J, Chang C. Application of data mining approaches to drug delivery. Adv Drug Deliv Rev 2006; 58:1409-30. [PMID: 17081647 DOI: 10.1016/j.addr.2006.09.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Accepted: 09/04/2006] [Indexed: 02/07/2023]
Abstract
Computational approaches play a key role in all areas of the pharmaceutical industry from data mining, experimental and clinical data capture to pharmacoeconomics and adverse events monitoring. They will likely continue to be indispensable assets along with a growing library of software applications. This is primarily due to the increasingly massive amount of biology, chemistry and clinical data, which is now entering the public domain mainly as a result of NIH and commercially funded projects. We are therefore in need of new methods for mining this mountain of data in order to enable new hypothesis generation. The computational approaches include, but are not limited to, database compilation, quantitative structure activity relationships (QSAR), pharmacophores, network visualization models, decision trees, machine learning algorithms and multidimensional data visualization software that could be used to improve drug delivery after mining public and/or proprietary data. We will discuss some areas of unmet needs in the area of data mining for drug delivery that can be addressed with new software tools or databases of relevance to future pharmaceutical projects.
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Affiliation(s)
- Sean Ekins
- ACT LLC, 1 Penn Plaza-36th Floor, New York, NY 10119, USA.
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Spasić I, Dunn WB, Velarde G, Tseng A, Jenkins H, Hardy N, Oliver SG, Kell DB. MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinformatics 2006; 7:281. [PMID: 16753052 PMCID: PMC1522028 DOI: 10.1186/1471-2105-7-281] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2005] [Accepted: 06/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5-6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behaviour of the cell can be observed using large-scale metabolomic studies. The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions. DESCRIPTION MeMo is a formal model for representing metabolomic data and the associated metadata. Two predominant platforms (SQL and XML) are used to encode the model. MeMo has been implemented as a relational database using a hybrid approach combining the advantages of the two technologies. It represents a practical solution for handling the sheer volume and complexity of the metabolomic data effectively and efficiently. The MeMo model and the associated software are available at http://dbkgroup.org/memo/. CONCLUSION The maturity of relational database technology is used to support efficient data processing. The scalability and self-descriptiveness of XML are used to simplify the relational schema and facilitate the extensibility of the model necessitated by the creation of new experimental techniques. Special consideration is given to data integration issues as part of the systems biology agenda. MeMo has been physically integrated and cross-linked to related metabolomic and genomic databases. Semantic integration with other relevant databases has been supported through ontological annotation. Compatibility with other data formats is supported by automatic conversion.
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Affiliation(s)
- Irena Spasić
- School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
| | - Warwick B Dunn
- School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
| | - Giles Velarde
- School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
| | - Andy Tseng
- School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
| | - Helen Jenkins
- Department of Computer Science, The University of Wales, Aberystwyth, SY23 3DB, UK
| | - Nigel Hardy
- Department of Computer Science, The University of Wales, Aberystwyth, SY23 3DB, UK
| | - Stephen G Oliver
- Faculty of Life Sciences, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
| | - Douglas B Kell
- School of Chemistry, Faraday Building, The University of Manchester, Manchester, M60 1QD, UK
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7
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Abstract
The rapid expansion of methods for measuring biological data ranging from DNA sequence variations to mRNA expression and protein abundance presents the opportunity to utilize multiple types of information jointly in the study of human health and disease. Organisms are complex systems that integrate inputs at myriad levels to arrive at an observable phenotype. Therefore, it is essential that questions concerning the etiology of phenotypes as complex as common human diseases take the systemic nature of biology into account, and integrate the information provided by each data type in a manner analogous to the operation of the body itself. While limited in scope, the initial forays into the joint analysis of multiple data types have yielded interesting results that would not have been reached had only one type of data been considered. These early successes, along with the aforementioned theoretical appeal of data integration, provide impetus for the development of methods for the parallel, high-throughput analysis of multiple data types. The idea that the integrated analysis of multiple data types will improve the identification of biomarkers of clinical endpoints, such as disease susceptibility, is presented as a working hypothesis.
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Affiliation(s)
- David M Reif
- Center for Human Genetics Research, Vanderbilt University Medical School, 519 Light Hall, Nashville, TN 37232-0700, USA.
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8
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Muthusamy B, Hanumanthu G, Suresh S, Rekha B, Srinivas D, Karthick L, Vrushabendra BM, Sharma S, Mishra G, Chatterjee P, Mangala KS, Shivashankar HN, Chandrika KN, Deshpande N, Suresh M, Kannabiran N, Niranjan V, Nalli A, Prasad TSK, Arun KS, Reddy R, Chandran S, Jadhav T, Julie D, Mahesh M, John SL, Palvankar K, Sudhir D, Bala P, Rashmi NS, Vishnupriya G, Dhar K, Reshma S, Chaerkady R, Gandhi TKB, Harsha HC, Mohan SS, Deshpande KS, Sarker M, Pandey A. Plasma Proteome Database as a resource for proteomics research. Proteomics 2005; 5:3531-6. [PMID: 16041672 DOI: 10.1002/pmic.200401335] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasma is one of the best studied compartments in the human body and serves as an ideal body fluid for the diagnosis of diseases. This report provides a detailed functional annotation of all the plasma proteins identified to date. In all, gene products encoded by 3778 distinct genes were annotated based on proteins previously published in the literature as plasma proteins and the identification of multiple peptides from proteins under HUPO's Plasma Proteome Project. Our analysis revealed that 51% of these genes encoded more than one protein isoform. All single nucleotide polymorphisms involving protein-coding regions were mapped onto the protein sequences. We found a number of examples of isoform-specific subcellular localization as well as tissue expression. This database is an attempt at comprehensive annotation of a complex subproteome and is available on the web at http://www.plasmaproteomedatabase.org.
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9
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Bala P, Georgantas RW, Sudhir D, Suresh M, Shanker K, Vrushabendra BM, Civin CI, Pandey A. TAGmapper: a web-based tool for mapping SAGE tags. Gene 2005; 364:123-9. [PMID: 16112519 DOI: 10.1016/j.gene.2005.05.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2005] [Revised: 05/04/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
Serial Analysis of Gene Expression (SAGE) is an important means of obtaining quantitative information about expression of genes in different samples. Short SAGE tags are 10 nucleotides long and often contain enough information to uniquely identify the gene(s) corresponding to the tag. We have observed, however, that the currently available resources are not adequate for accurate mapping of all SAGE tags to genes. Here, we describe development of a web-based tool called TAGmapper (http://tagmapper.ibioinformatics.org), which provides a comprehensive and accurate mapping of SAGE tags to genes. We were able to map SAGE tags accurately in several instances where two other popular resources, SAGEmap (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and SAGE Genie (http://cgap.nci.nih.gov/SAGE), provided incorrect or no assignment of tags to genes. Finally, we experimentally determined the expression of a subset of genes assigned by TAGmapper using DNA microarrays and/or quantitative PCR to confirm the reliability of the gene mappings. We anticipate that TAGmapper will be a useful tool in functional genomic approaches by providing accurate identification of genes in SAGE experiments.
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Affiliation(s)
- P Bala
- Institute of Bioinformatics, International Tech Park, Whitefield Road, Bangalore 560 066, India
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10
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Väliaho J, Riikonen P, Vihinen M. Distribution of immunodeficiency fact files with XML--from Web to WAP. BMC Med Inform Decis Mak 2005; 5:21. [PMID: 15978138 PMCID: PMC1184081 DOI: 10.1186/1472-6947-5-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Accepted: 06/26/2005] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at http://bioinf.uta.fi/idr/. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at http://bioinf.uta.fi/idml/.
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Affiliation(s)
- Jouni Väliaho
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
| | - Pentti Riikonen
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
- Department of Information Technology, University of Turku, FI-20520 Turku, Finland
| | - Mauno Vihinen
- Institute of Medical Technology, FI-33014 University of Tampere, Finland
- Research Unit, Tampere University Hospital, FI-33520 Tampere, Finland
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11
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Ekins S, Kirillov E, Rakhmatulin EA, Nikolskaya T. A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism. Drug Metab Dispos 2004; 33:474-81. [PMID: 15608136 DOI: 10.1124/dmd.104.002717] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The increasing generation of biological data represents a challenge to understanding the complexity of systems, resulting in scientists increasingly focused on a relatively narrow area of study, thereby limiting insight that can be gained from a broader perspective. In the field of drug metabolism and toxicology we are witnessing the characterization of many proteins. Most of the key enzymes and transporters are recognized as transcriptionally regulated by the nuclear hormone receptors such as pregnane X receptor, constitutive androstane receptor, vitamin D receptor, glucocorticoid receptor, and others. There is apparent cross talk in regulation, since multiple receptors may modulate expression of a single enzyme or transporter, representing one of many areas of active research interest. We have used published data on nuclear hormone receptors, enzymes, ligands, and other biological information to manually annotate an Oracle database, forming the basis of a platform for querying (MetaDrug). Using algorithms, we have demonstrated how nuclear hormone receptors alone can form a network of direct interactions, and when expanded, this network increases in complexity to describe the interactions with target genes as well as small molecules known to bind a receptor, enzyme, or transporter. We have also described how the database can be used for visualizing high-throughput microarray data derived from a published study of MCF-7 cells treated with 4-hydroxytamoxifen, to highlight potential downstream effects of molecule treatment. The database represents a novel knowledge mining and analytical tool that, to be relevant, requires continual updating to evolve alongside other key storage systems and sources of biological knowledge.
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Affiliation(s)
- Sean Ekins
- Computational Biology, GeneGo, Inc, 500 Renaissance Drive, Suite 106, St. Joseph, MI 49085, USA.
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Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia 2004; 6:1-6. [PMID: 15068665 PMCID: PMC1635162 DOI: 10.1016/s1476-5586(04)80047-2] [Citation(s) in RCA: 2785] [Impact Index Per Article: 139.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA microarray technology has led to an explosion of oncogenomic analyses, generating a wealth of data and uncovering the complex gene expression patterns of cancer. Unfortunately, due to the lack of a unifying bioinformatic resource, the majority of these data sit stagnant and disjointed following publication, massively underutilized by the cancer research community. Here, we present ONCOMINE, a cancer microarray database and web-based data-mining platform aimed at facilitating discovery from genome-wide expression analyses. To date, ONCOMINE contains 65 gene expression datasets comprising nearly 48 million gene expression measurements form over 4700 microarray experiments. Differential expression analyses comparing most major types of cancer with respective normal tissues as well as a variety of cancer subtypes and clinical-based and pathology-based analyses are available for exploration. Data can be queried and visualized for a selected gene across all analyses or for multiple genes in a selected analysis. Furthermore, gene sets can be limited to clinically important annotations including secreted, kinase, membrane, and known gene-drug target pairs to facilitate the discovery of novel biomarkers and therapeutic targets.
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Affiliation(s)
- Daniel R Rhodes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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13
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Abstract
Mass spectrometry is already established as the method of choice for protein identification. Hitherto, a major limitation of mass spectrometry was the inability to quantitate protein levels. With the development of novel methods, such as the AQUA method by Gerber et al., this hurdle has finally been overcome, unleashing the power of mass spectrometry to study protein dynamics in cells.
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Affiliation(s)
- Chaerkady Raghothama
- Institute of Bioinformatics, Discoverer Unit 1, International Tech Park Ltd, Bangalore 560-066, India
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14
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Navarro JD, Talreja N, Peri S, Vrushabendra BM, Rashmi BP, Padma N, Surendranath V, Jonnalagadda CK, Kousthub PS, Deshpande N, Shanker K, Pandey A. BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics 2004; 5:43. [PMID: 15099404 PMCID: PMC406495 DOI: 10.1186/1471-2105-5-43] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2003] [Accepted: 04/20/2004] [Indexed: 11/10/2022] Open
Abstract
Background The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. Results BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database , a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. Conclusions As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.
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Affiliation(s)
- J Daniel Navarro
- McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, U.S.A
- Departamento de Automática y Computación, Área de Ciencias de la Computación e Inteligencia Artificial, Universidad Pública de Navarra, 31006, Pamplona, Spain
| | - Naveen Talreja
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - Suraj Peri
- McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, U.S.A
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - BM Vrushabendra
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - BP Rashmi
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - N Padma
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - Vineeth Surendranath
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - Chandra Kiran Jonnalagadda
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - PS Kousthub
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - Nandan Deshpande
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - K Shanker
- Institute of Bioinformatics, Discoverer 7Floor, International Technology Park Ltd., Bangalore 560 066, India
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, U.S.A
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16
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Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TKB, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res 2004; 32:D497-501. [PMID: 14681466 PMCID: PMC308804 DOI: 10.1093/nar/gkh070] [Citation(s) in RCA: 406] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein-protein interactions, post-translational modifications, enzyme-substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.
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Affiliation(s)
- Suraj Peri
- McKusick-Nathans Institute of Genetic Medicine and Department of Biological Chemistry, Johns Hopkins University, Baltimore, MD 21287, USA
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Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TKB, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JGN, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res 2003; 13:2363-71. [PMID: 14525934 PMCID: PMC403728 DOI: 10.1101/gr.1680803] [Citation(s) in RCA: 747] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era.
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Affiliation(s)
- Suraj Peri
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21287, USA
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Lundgren DH, Eng J, Wright ME, Han DK. PROTEOME-3D: an interactive bioinformatics tool for large-scale data exploration and knowledge discovery. Mol Cell Proteomics 2003; 2:1164-76. [PMID: 12960178 PMCID: PMC1487189 DOI: 10.1074/mcp.m300059-mcp200] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Comprehensive understanding of biological systems requires efficient and systematic assimilation of high-throughput datasets in the context of the existing knowledge base. A major limitation in the field of proteomics is the lack of an appropriate software platform that can synthesize a large number of experimental datasets in the context of the existing knowledge base. Here, we describe a software platform, termed PROTEOME-3D, that utilizes three essential features for systematic analysis of proteomics data: creation of a scalable, queryable, customized database for identified proteins from published literature; graphical tools for displaying proteome landscapes and trends from multiple large-scale experiments; and interactive data analysis that facilitates identification of crucial networks and pathways. Thus, PROTEOME-3D offers a standardized platform to analyze high-throughput experimental datasets for the identification of crucial players in co-regulated pathways and cellular processes.
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Affiliation(s)
- Deborah H. Lundgren
- From the Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, Farmington, CT 06030, and
| | - Jimmy Eng
- Institute for Systems Biology, Seattle, WA 98103
| | | | - David K. Han
- From the Center for Vascular Biology, Department of Physiology, University of Connecticut School of Medicine, Farmington, CT 06030, and
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