- Data Sources
The International Aging Research Portfolio (IARP) is an independent initiative serving the aging research community, academic, corporate, patient advocacy and charitable funding organizations worldwide.
The AgingPortfolio.Org system is a flexible and highly scalable knowledge management system developed to enable funding organizations to collaborate, track, analyze, structure, make decisions and set directions for future research efforts in aging and also address the needs of research investigators, health care policy makers, government officials, interest groups and general public.
The goal of the International Aging Research Portfolio is to become a centralized portal for aging research providing highly granular relevant information to scientists, funding organizations, policy makers and providing a platform for collaboration and research.
At present, IARP incorporates databases of grants from multiple sources such as the NIH, European Commission, CIHR, and MRC. It also incorporates MEDLINE publication abstracts under a license from the National Library of Medicine.
The database contains millions of research projects with funding information and is fully searchable. The system also provides a categorized directory for the aging research projects. In addition to the manual classification by the SAB members, the system uses semantic classification algorithms to automatically classify projects into research areas related to aging.
The flexibility of the system provides different views on aging and age-related projects in order to find trends and analyze the current status of the investigations. It also gives the opportunity to build new classification taxonomies to look at the problem of aging research at different points. Thus, the first centralized system for tracking such complex, interdisciplinary and controversial area as aging research was developed and made available to the public via AgingPortfolio.org.
Please cite the IARP papers:
Zhavoronkov, A., & Cantor, C. R. (2011). Methods for structuring scientific knowledge from many areas related to aging research. PloS one, 6(7), e22597. doi:10.1371/journal.pone.0022597
Methods for Structuring Scientific Knowledge from Many Areas Related to Aging Research
Kolesov, A., Kamyshenkov, D., Litovchenko, M., Smekalova, E., Golovizin, A., & Zhavoronkov, A. (2014). On Multilabel Classification Methods of Incompletely Labeled Biomedical Text Data. Computational and Mathematical Methods in Medicine, 2014. doi:10.1155/2014/781807
On Multilabel Classification Methods of Incompletely Labeled Biomedical Text Data
External link: about
The Scientific Advisory Board for IARP is currently being formed. This section will be populated before the system becomes available to the general public.
To start using the system with the SAB privileges the invited member must register.
The SAB is formed by invitation only. The SAB chair is Dr. Charles Cantor (www.charlescantor.org).
Invited SAB members can refer other scientists to join the SAB. To join the SAB, a confirmation via email is required.
The SAB administrative interface is very different from the general user interface. The SAB members can:
- Classify projects into categories within the current taxonomy
- Propose new categories to be created
- Add/approve category editors
- Train the AI classification algorithms by creating training sets for specific categories.
- Discuss the projects with other SAB member
External link: sab
Since June 2008 the IARP system went through several design and prototyping stages as the quality and granularity of the source data improved. Excluding the SAB members over 40 experts from many fields of knowledge including biology, psychology, computer science, engineering and economics contributed to the project on the volunteer basis. As IARP continues its relentless pursuit for new data, methods for converting the data into useful knowledge in aging research and development of scientific collaboration tools, we will continue adding the team member biographies. In the case that you would like to become a part of the development team or collaborate in any other way to help advance research into aging and age-related diseases, please Contact Us.
|Alexander Zhavoronkov, PhD||Project Director|
Before bringing together a team to collaborate on the Aging Research Portfolio in 2008, Alex had a successful career as the director at ATI Technologies, president of Mediox and the director of business development at GTCbio. He also served as a consultant to Sequenom and to Colby Pharmaceutical Company.
He currently serves as the director and trustee of the Biogerontology Research Foundation, a UK-based charity supporting aging research internationally and heads NeuroG, a neuroinformatics project intended to assist the elderly suffering from dementia.
Alex holds BCom (finance/operations) and BSc (computer science) degrees from Queen’s University, MS (biotechnology) degree from Johns Hopkins University and a PhD(biophysics) from the Moscow State University, Physics Faculty.
The development of the International Aging Research Portfolio was made possible by the collective volunteer effort of many experts in the fields of biology, mathematics, computer science, engineering, psychology and economics. To date the project received no public, NGO or corporate funding.
|Konstantin Romantsov||Technical Director|
Since 2000 Konstantin Romantsov develops and manages Internet projects. In 2002 he joined the Nienschanz Group as the head of IS engineering, where he designed and developed high-performance high-redundancy cluster systems. In 2004 he joined Altell Corporation as the technical director, where he supervised the development of many secure communications systems for large corporate clients and the government. In 2007 he founded ITSKY, a developer of open-source solutions for public use.
Konstantin graduated from the St. Petersburg State University of Telecommunications with a masters degree in engineering.
Konstantin joined the International Aging Research Portfolio in March 2010 reporting to Dr. Zhavoronkov and brought the project from the prototyping stage to live status. He managed complex tasks such as the NIH and EC data processing and mapping, server-side development and the transition of the project from a distributed hosting architecture into the Amazon EC2 cloud. He is currently working on the project full time coordinating the work of the geographically-distributed international team of highly-motivated and creative mathematicians, algorithm designers and system developers.
|Eli Mohamad||Head of Communications|
Eli received his BSc in Service Management from Rochester Institute of Technology, NY, and his MSc in Technology and Innovation Management from SPRU, University of Sussex, UK.
His work focuses on management of projects financed from international development funds (EU, World Bank, etc.) and improving innovation processes for public and private institutions. He is experienced in many aspects of commercialization of innovation, technology transfer and fundraising for innovative concepts, and has worked extensively in the USA, UK, Cuba, and Western Balkan countries.
Eli joined the IARP in November 2009 and is responsible for communication and maintenance of networks with the public institutions.
|Zeljka Smit-McBride, PhD||Pathway Visualization and IARP Labs|
Dr. Smit-McBride has had a sustained interest in the underlying molecular mechanisms governing life and how their disturbance can lead to aging or disease. Her interest in systems biology arose from the goal to determine why aging is such a dominant risk factor for many ailments such as cancer, neurodegenerative disease, arthritis, etc. Currently, her research focus is on age-related macular degeneration. To determine the underlying defects associated with this disease Dr. Smit-McBride have chosen to explore the genomics and epigenetics of retinal tissue during a normal aging process vs. degenerative aging process.
Dr. Smit-McBride is currently an Associate Project Scientist in the Department of Ophthalmology at School of Medicine, University of California at Davis. Dr. Smit-McBride holds B.S. in molecular biology and physiology and M.S. in genetics both from the University of Belgrade, and Ph.D. in genetics from University of California at Davis.
Throughout her successful career Dr. Smit-McBride have participated and contributed significantly in the fields of cancer biology, immunology of AIDS, and more recently, aging and age-related disorders of the eye. She has extensive research expertise in various aspects of molecular biology of nucleic acids, as well as experience in protein biochemistry and immunology. In addition, she is skilled in bioinformatics data analysis of Affymetrix microarrays as well as biological pathways analysis with GeneSpring and Ingenuity Pathways Analysis software. Dr. Smit-McBride is author of many scientific papers published in peer reviewed journals. Role in the International Aging Portfolio: Editor of the classification and visual representation of the aging theories and corresponding research projects.
|Developers and Significant Contributors:|
|Olga Koborova, PhD-candidate||Project Manager|
Olga Koborova received a masters degree in biotechnology from the Moscow State University, Faculty of Bioengineering and Bioinformatics. During her studies at MSU she conducted research at the Moscow Oncology Institute. She conducted research and is presently employed at the Institute of Biomedical Chemistry in Moscow and is participating in the European breast cancer drug development project Net2Drug.
Presently she is working towards a PhD at the Institute of Biomedical Chemistry. Her research interests include bioinformatics, systems biology, pathway design and analysis and identification of cancer drug targets.
*Role in the project: First project manager of IARP, joining the project in January 2009 reporting to Dr. Zhavoronkov. Supervised the development of the first system prototype and participated in all stages of system design and development, managed a geographically-distributed team of experts in the diverse fields of knowledge. Together with Dr. Zhavoronkov and Eli Mohamad participated in the first top-level meeting with the Publications Office of the European Commission in Luxembourg resulting in successful transfer of grant databases. Prepared and condicted a survey of over 1,000 scientists to identify specific system requirements.
In August 2010 Olga took a leave of absence from the project to focus on completing her PhD dissertation.
|Anton Yu Kolesov, PhD-candidate||Team Leader, Classification|
Anton Yu Kolesov holds a masters degree from the Moscow State University, Mechanics and Mathematics Faculty. He also completed a masters program at the Yandex School of Data Analysis. Anton is working towards a PhD at the Yaroslavl State University doing research in Machine Learning, Text Classification, Intelligent Information Systems.
*Role in the project: automatic project and publication classifiers, integration of VSS and BFA methods, intelligent matching of grants to publications and other data.
|Varvara Konova, MD-candidate||Classification Engineer|
Varvara is expecting to graduate from the MD program at the Russian State Medical University. Her research interests include bioinformatics, systems biology of aging and age-related diseases.
*Role in the project: training the AI system to recognize projects related to aging and classifying the projects by their relationship to specific categories, development of the training sets for automatic classification, and validating the data sets.
|Kirill Alyavdin||Head of outreach and communications, Eastern Europe|
Kirill Alyavdin is the head of corporate communications at S7 Airlines, one of the leading international air carriers and a member of oneworld global alliance. Prior to joining S7 Airlines, Kirill served as the head of marketing and brand promotion and the press secretary of Mobile TeleSystems (MTS) (NYSE: MBT). His prior experience includes the executive-level press secretary position with Rostelecom, Russia's largest national telecommunications operator and and head of communication department of Depo Computers, leading Russia’s PC manufacturer. He has significant experience in many aspects of corporate and consumer communications, long term media relations, crisis PR, development and implementation of communication strategies, PR budgeting and event management.
*Role in the project:Head of communications, public relations and outreach in Eastern Europe including Russia & CIS
|Pavel Yu. Polyakov, PhD-candidate||Programmer|
Pavel Yu. Polyakov received the B.E.E. and M.S.E.E. degrees in applied physics and mathematics from Moscow Institute of Physics and Technology. Currently, he is working towards the Ph.D. degree at the Scientific-Research Institute for System Studies, Russian Academy of Sciences. He is a member of the Russian Context Optimizer research group. His research focuses on simulation of brain concept learning by recurrent neural networks.
*Role in the project: development of the unsupervised topic detector tool based on Boolean Factor Analysis (BFA) method
|Chris Smelick, MD-candidate||Consultant, System Validation|
Chris Smelick is working towards the MD degree at at the University of North Carolina at Chapel Hill Medical School. Before medical school Chris worked as the Chief Bioengineer at ImmunePath, founded the Vitae Institute to promote aging research. He currently serves as the vice-president of the Elata Foundation for promoting rTMS research.
Chris received the M.A. degree from Boston University in Medical Sciences, and a B.S. in biochemistry from UNC Chapel Hill.
*Role in the project: testing and system validation, advice on system development
|David Asprey, MBA||Consultant, Server Infrastructure|
Dave Asprey is an independent consultant working with technology startups and VCs. He focuses on strategy, product marketing, business development, and IT, with a strong expertise in web hosting, networking, monitoring & management, security, and performance and availability. Dave recently completed five years at Exodus Communications (acquired by Cable & Wireless), where he was Director of Strategic Planning. Previously, he was with 3Com Corporation as an Internet Architect.
Dave has an MBA from Wharton and a BS in Computer Information Systems from California State University.
*Role in the project: adviced on server architecture, recommended using cloud computing infrastructure for computationally-intensive tasks
Dmitry G. Ivanov works as a team leader at NJ, US-based software development company Envisionext Inc. Dmitry has a masters degree in engineering sciences from Odessa National Polytechnic University and an advanced degree in software development from STEP Computer Academy.
*Role in the project: code review, refactoring, optimizations, direct development
Grigory Vaigandt heads Neoviso, a software deelopment company in Gomel Belarus. Grigory started his career as the PHP developer in 1999. In 2004 he became the development team lead and then technical manager at Envisionext Inc. In 2009 he starteh a softwae development company.
Grigory holds two graduate degrees in computer science from the IT faculty at Gomel State Technical University and in management at Belarusian Trade and Economics University.
*Role in the project: site design, quick search, trends, various small tasks and DB issues
|Russell Han||Graphic Designer|
Russell Han is the founder/creative director of Hansbro Studio, a graphic design team that focuses on developing corporate identity for start-ups. His expertise includes art direction, corporate identity design, print design and web design. He has worked as a graphic designer and art director in the advertising, technology and education industries since 2000. Currently, he leads a team of graphic designers to help start-ups develop their own corporate identity and provides branding consultancy.
*Role in the project: advice on the identity of the IARP, web design
|Jane Yang||Graphic Designer and Coordinator|
Jane Yang is the project manager of Hansbro Studio, a graphic design team that focuses on developing corporate identity for start-ups. She works as a coordinator between the graphic design team at Hansbro Studio and other members of the IARP. She received a masters degree in linguistics from Beijing Foreign Studies University. Since her graduation in 2007, she has been worked as a project manager at the Multimedia Production Department of Pearson Education Asia and Hansbro Studio.
*Role in the project: facilitated the communication between the graphic design team and the tech team, advice on the web design
|Vasilisa Rudneva||Validation Engineer|
In 2011 Vasilisa Rudneva is expected to graduate from Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics and is currently one of the top ten students in her class. Since 2006 she is working as a researcher at Laboratory of Lipid Systems Biology, A.N.Belozersky Institute of Physico-Chemical Biology. Her main academic interests are pathway design and analysis, protein-protein interactions and gene expression analysis using microarray data. After taking part in Aging Research Portfolio project Vasilissa developed a strong interest in data mining and data analysis in biotechnology.
*Role in the project: System Validation
|Valeriya Kolesnikova, M.S.-candidate||Validation Engineer|
Valeriya Kolesnikova is a student at the Lomonosov Moscow State University, Department of Bioengineering and Bioinformatics. Her current research is focused on Programmed Cell Death (PCD) in plants with the emphasis on the role of cell death marker in Nicotiana benthamiana(NbCDM). Since 2008 she is working as a research scientist at the laboratory for nucleic acid-protein interactions, A.N.Belozersky Institute of Physico-Chemical Biology. She also participates in collaborative projects with the Blokhin Russian Cancer Research Center. Her main research interests are biochemistry, regenerative medicine and bioinformatics of aging with the focus on data mining and knowledge management systems.
*Role in the project: Validation, testing, outreach. Current project includes biotechnology conference linking and classification
|Ekaterina Gushchanskaya, PhD-candidate||Training sets and Project management|
Ekaterina is working towards a PhD at the Institute of Gene Biology, Russian Academy of Science. Her research interests include cell and molecular biology, particularly chromatin organization of eucariotic cells.
She holds a masters degree in biological sciences from the Moscow State University.
*Role in the project: Created reference and training sets for the SVM algorithm. Coordinated the communication with key SAB members.
External link: developers
The system contains a compiled database of projects funded by the National Institutes of Health and the European Commission and uses semantic classification algorithms to automatically classify projects into research areas related to aging. It also contains MEDLINE article abstracts under a license from the National Library of Medicine.
The first working prototype of Aging Portfolio was created in August 2009 using CORDIS data sets collected from the NIH website. However, in 2009 the NIH started transitioning to a new system called the RePORT. On November 5th 2009 we first met with the NIH office of the director and the developers of RePORT to get access to the more granular funding data sets. The NIH agreed to put the data in the public domain, but went through many revisions and format changes. It took our team over a year to integrate the data into the system as it was processed for integration into the new NIH reporting system. We are constantly making adjustments and changes to keep up to date with the NIH databases. In the case that you notice any corrupt data in the project descriptions, please notify us as soon as possible using the contact form of the website.
On April 25th 2010 we met with the Publications Office of the European Commission and got access to the highly granular project funding data. Most of the EC grants are awarded to international research teams and span several years. To integrate this data into our database and make it more granular, we split the funding amounts among the investigators and equally divided the funding by the number of years in the program. This may cause some discrepancies in the results generated by the Aging Portfolio System, which re-assembles these projects in the directory of classified categories, but returns partial results when searching for projects during specific years.
The MEDLINE publication abstracts data was licensed from the NLM and is currently in the database. It will take time to properly link the publications to grants, apply the automatic classification algorithms and create links between publications, investigators and grants.
We would like to thank the NIH and EC CORDIS for making the funding data available.
External link: data sources