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Toward an interactive article: integrating journals and biological databases

Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S Skrzypek, Steven J Marygold, Raymund Stefancsik (+3 others)
2011 BMC Bioinformatics  
Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery.  ...  Results: We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD) WormBase.  ...  Authors' contributions AR developed, maintains and runs the linking software and the software for obtaining the entities from the biological databases.  ... 
doi:10.1186/1471-2105-12-175 pmid:21595960 pmcid:PMC3213741 fatcat:icntu6fksnfjdpbwzlva6xmysa

Curating gene sets: challenges and opportunities for integrative analysis

2019 Database: The Journal of Biological Databases and Curation  
, diseases, drug interactions or environmental conditions.  ...  from publicly available resources and published gene lists.  ...  Acknowledgements The authors would like to thank Robert Burgess, Emily Spaulding and Beena Kadhakhuza for their suggestions and comments toward this work.  ... 
doi:10.1093/database/baz036 pmid:30888410 pmcid:PMC6424415 fatcat:kmdztwbfr5fajlemdp4xgvvc5u

KOFFI and Anabel 2.0-a new binding kinetics database and its integration in an open-source binding analysis software

2019 Database: The Journal of Biological Databases and Curation  
To date, over 270 articles were manually curated and binding data on over 1705 interactions was collected and stored in the (KOFFI) database.  ...  The kinetics of featured interactions (KOFFI) database is a novel tool and resource for binding kinetics data from biomolecular interactions.  ...  Acknowledgements We thank Normann Kilb, Lisa-Marie Sehls, Philipp Andreas Meyer and Jürgen Burger of ZBSA Center for Biological Systems Analysis, University of Freiburg for their support during the annotation  ... 
doi:10.1093/database/baz101 pmid:31608948 pmcid:PMC6790968 fatcat:rwxvaia2pzfx3ccuvqqvli65ta

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

Zhi-Ping Liu, Canglin Wu, Hongyu Miao, Hulin Wu
2015 Database: The Journal of Biological Databases and Curation  
RegNetwork: an integrated database of transcriptional and posttranscriptional regulatory networks in human and mouse.  ...  Therefore, in this work, we build a knowledge-based database, named 'RegNetwork', of gene regulatory networks for human and mouse by collecting and integrating the documented regulatory interactions among  ...  Conclusion In this article, we developed a database, RegNetwork, of the knowledge-based genome-wide regulatory networks in human and mouse by integrating various data sources.  ... 
doi:10.1093/database/bav095 pmid:26424082 pmcid:PMC4589691 fatcat:iax5idoulfad7iz4z5iqmn4swu

Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes

2019 Database: The Journal of Biological Databases and Curation  
Visualization of intricate biological networks is an important feature which utilizes the Neo4j Graph database making analysis of relationships and long-range system viewing possible.  ...  An understanding of the integrative and spatio-temporal impact of these regulatory factors can provide better insights into the state of a 'cell system'.  ...  We are thankful to Dr Amita Bhattacharya and Dr SK Vats for the English editing. The CSIR-IHBT article communication ID number for this MS is 3575.  ... 
doi:10.1093/database/baz130 pmid:31796964 pmcid:PMC6891001 fatcat:5nd2hq4pjzaprad2xfwlfum3eq

GenoSurf: metadata driven semantic search system for integrated genomic datasets

2019 Database: The Journal of Biological Databases and Curation  
as part of an integrated query answering system for performing complex queries over genomic regions and metadata.  ...  Currently, GenoSurf integrates about 40 million metadata of several major valuable data sources, including three providers of clinical and experimental data (TCGA, ENCODE and Roadmap Epigenomics) and two  ...  Acknowledgement We wish to thank all collaborators who participated to our evaluation survey and thus allowed us to assess and improve the system. Conflict of interest. None declared.  ... 
doi:10.1093/database/baz132 pmid:31820804 pmcid:PMC6902006 fatcat:gf4llmuty5ev5fdydmbra45tti

Argo: an integrative, interactive, text mining-based workbench supporting curation

R. Rak, A. Rowley, W. Black, S. Ananiadou
2012 Database: The Journal of Biological Databases and Curation  
Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline  ...  To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing  ...  Acknowledgements The authors would like to specially thank BalaKrishna Kolluru and Riza Theresa Batista-Navarro who provided access to the enzyme-drug annotation task they supervise, which was used to  ... 
doi:10.1093/database/bas010 pmid:22434844 pmcid:PMC3308166 fatcat:pb5yv7qtsff6jf3be3ps4quqxq

In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research

Ankit Sharma, Vrushali Deshpande, Madankumar Ghatge, Rajani Kanth Vangala
2017 Database: The Journal of Biological Databases and Curation  
In order to provide comprehensive information from hitherto dispersed data, we developed an integrative knowledgebase called "In-Cardiome or Integrated Cardiome" for all the stake holders in healthcare  ...  One major hurdle in the improvement of diagnosis and treatment for CAD is the lack of integration of knowledge from different areas of research like molecular, clinical and drug development.  ...  Sponsors had no role in the design, conduct, sample collection, analysis and interpretation of the data or in the preparation, review or approval of the article. Conflict of interest.  ... 
doi:10.1093/database/bax077 pmid:29220465 pmcid:PMC5737197 fatcat:sn5oj3ecand55dgycgf3crf5oe

Evidence classification of high-throughput protocols and confidence integration in RegulonDB

Verena Weiss, Alejandra Medina-Rivera, Araceli M. Huerta, Alberto Santos-Zavaleta, Heladia Salgado, Enrique Morett, Julio Collado-Vides
2013 Database: The Journal of Biological Databases and Curation  
Database URL: http://regulondb.ccg.unam.mx/ .  ...  To integrate these data into RegulonDB, we present two strategies for the evaluation of confidence, statistical validation and independent cross-validation.  ...  Acknowledgements We are grateful to Yalbi Balderas for the TF conformation cross-validation discussion, to Stephen Busby for suggesting the introduction of the third confidence level confirmed, and we  ... 
doi:10.1093/database/bas059 pmid:23327937 pmcid:PMC3548332 fatcat:n6lv33ocxzfpne4ncrt5iqoodi

ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs)

Smriti Mishra, Mohammad I Shah, Malay Sarkar, Nimisha Asati, Chittaranjan Rout
2018 Database: The Journal of Biological Databases and Curation  
This resource contains literature-curated disease candidate genes (DCGs) enriched with various regulatory elements that have been generated using an integrated bioinformatics workflow of databases searches  ...  Therefore, the first genetic knowledge resource, ILDgenDB, has been developed with an objective to provide ILDs genetic data and their integrated analyses for the better understanding of disease pathogenesis  ...  Khan and Dr Amit Das for the longstanding support. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay053 pmid:29897484 pmcid:PMC6007225 fatcat:3nclq6nxajdtljteell33detn4

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

Matyas F. Cserhati, Sanjit Pandey, James J. Beaudoin, Lorena Baccaglini, Chittibabu Guda, Howard S. Fox
2015 Database: The Journal of Biological Databases and Curation  
We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated,  ...  The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases.  ...  We would also like to acknowledge Eamonn Maguire from ISAtools in giving advice in setting up the database. Funding This work was funded by an NNTC-DCC grant to H.S.F., number 5U24MH100925-02.  ... 
doi:10.1093/database/bav074 pmid:26228431 pmcid:PMC4520230 fatcat:6u26gsulubgxbjvzsxxfhtswcu

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

Michele Tinti, Fábio Madeira, Gavuthami Murugesan, Gerta Hoxhaj, Rachel Toth, Carol MacKintosh
2014 Database: The Journal of Biological Databases and Curation  
Margaret Malcolm for assistance in sorting the human kinome into 2R-ohnologue families; the DNA Sequencing Service at the College of Life Sciences, University of Dundee, coordinated by Nicholas Helps; and  ...  Page 5 of 15 Database, Vol. 2014, Article ID bat085, doi:10.1093/database/bat085 Original article ... ..... Database, Vol. 2014, Article ID bat085, doi:10.1093/database/bat085 ...  ...  Database, Vol. 2014, Article ID bat085, doi:10.1093/database/bat085 Page 12 of 15 Original article  ... 
doi:10.1093/database/bat085 pmid:24501395 pmcid:PMC3914767 fatcat:v4dh3p5tnbbf5c3gyda4xl4m2e

The Histone Database: an integrated resource for histones and histone fold-containing proteins

L. Marino-Ramirez, K. M. Levine, M. Morales, S. Zhang, R. T. Moreland, A. D. Baxevanis, D. Landsman
2011 Database: The Journal of Biological Databases and Curation  
Acknowledgments The Histone Database update utilized the highperformance computational capabilities of the Biowulf Linux cluster at the National Institutes of Health, Bethesda, Maryland.  ...  Funding Funding for open access charge: The Intramural Research Programs of the National Center for Biotechnology Information, National Library of Medicine and the National Human Genome Research Institute  ...  Histone proteins and their variants have an This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http:// creativecommons.org/licenses/by-nc  ... 
doi:10.1093/database/bar048 pmid:22025671 pmcid:PMC3199919 fatcat:6rmx4pxrijdxrdfxveuvelgz3e

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

Huilei Xu, Caroline Baroukh, Ruth Dannenfelser, Edward Y. Chen, Christopher M. Tan, Yan Kou, Yujin E. Kim, Ihor R. Lemischka, Avi Ma'ayan
2013 Database: The Journal of Biological Databases and Curation  
The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers  ...  Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse highthroughput studies including chromatin immunoprecipitation  ...  Several databases and tools have been published to facilitate the integration of such data (1) (2) (3) (4) (5) (6) (7) (8) (9) , and such efforts pave the way toward an in silico reconstruction of the  ... 
doi:10.1093/database/bat045 pmid:23794736 pmcid:PMC3689438 fatcat:3wzdumoanbf75pdo3xxuqaywjy

Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes

Navneet Tomar, Akhilesh Mishra, Nirotpal Mrinal, B. Jayaram
2016 Database: The Journal of Biological Databases and Curation  
Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes.  ...  Here, we present Onco-Regulon (http://www.scfbio-iitd.res.in/ software/onco/NavSite/index.htm), an integrated database of regulatory motifs of cancer genes clubbed with Unique Sequence-Predictor (USP)  ...  This software USP is an attempt towards this goal.  ... 
doi:10.1093/database/baw116 pmid:27515825 pmcid:PMC4980569 fatcat:vsshsxl2rnaylabtlein6ew62i
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