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Managing biological complexity across orthologs with a visual knowledgebase of documented biomolecular interactions

Vincent VanBuren, Hailin Chen
2012 Scientific Reports  
Distributing the responsibility for maintenance of a knowledgebase to a community of subject matter experts is an effective strategy for large, complex and rapidly changing knowledgebases.  ...  Cognoscente was motivated by the need to (1) update the knowledgebase of biomolecular interactions at the user level, and (2) flexibly visualize multi-molecule query results for heterogeneous interaction  ...  The corpus of knowledge of biomolecular interactions differs in coverage for different model organisms.  ... 
doi:10.1038/srep01011 pmid:23264875 pmcid:PMC3527363 fatcat:oml7dotelvbqnlwka6e4cu4634

Getting Started in Biological Pathway Construction and Analysis

Ganesh A Viswanathan, Jeremy Seto, Sonali Patil, German Nudelman, Stuart C Sealfon, Olga Troyanskaya
2008 PLoS Computational Biology  
BIND, Biomolecular Interaction Network Database; BioPP, Biological Pathway Publisher; DIP, Database of Interacting Proteins; EcoCyc, Encyclopaedia of E. coli Genes and Metabolism; GNPV, Genome Network  ...  SBML, which is used mainly for representation of pathways and mathematical models and supported by more than 100 software systems, is currently the best-suited format for mathematical modeling and simulations  ... 
doi:10.1371/journal.pcbi.0040016 pmid:18463709 pmcid:PMC2323403 fatcat:dldyxs5cdbabpbf23srfddtbye

NetWalker: a contextual network analysis tool for functional genomics

Kakajan Komurov, Serkan Dursun, Serkan Erdin, Prahlad T Ram
2012 BMC Genomics  
Functional analyses of genomic data within the context of a priori biomolecular networks can give valuable mechanistic insights.  ...  However, such analyses are not a trivial task, owing to the complexity of biological networks and lack of computational methods for their effective integration with experimental data.  ...  The NIK is a pre-compiled knowledgebase of human genes, their functional annotations and their biomolecular interactions.  ... 
doi:10.1186/1471-2164-13-282 pmid:22732065 pmcid:PMC3439272 fatcat:cdof36tqsvdvbdc7m6ha2eoyoi

Reactome graph database: Efficient access to complex pathway data

Antonio Fabregat, Florian Korninger, Guilherme Viteri, Konstantinos Sidiropoulos, Pablo Marin-Garcia, Peipei Ping, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob, Timothée Poisot
2018 PLoS Computational Biology  
Author summary To better support genome analysis, modeling, systems biology and education, we now offer our knowledgebase of biomolecular pathways as a graph database.  ...  Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways.  ...  Reactome annotates processes in a consistent pathway model to create an online resource for researchers as a core reusable pathway dataset for systems biology approaches.  ... 
doi:10.1371/journal.pcbi.1005968 pmid:29377902 pmcid:PMC5805351 fatcat:7znckpg5a5cnrfeekcmakdieyy

UniCarbKB: Putting the pieces together for glycomics research

Matthew P. Campbell, Catherine A. Hayes, Weston B. Struwe, Marc R. Wilkins, Kiyoko F. Aoki-Kinoshita, David J. Harvey, Pauline M. Rudd, Daniel Kolarich, Frederique Lisacek, Niclas G. Karlsson, Nicolle H. Packer
2011 Proteomics  
UniCarbKB is an initiative that aims to promote the creation of an online information storage and search platform for glycomics and glycobiology research.  ...  The knowledgebase will offer a freely accessible and information-rich resource supported by querying interfaces, annotation technologies and the adoption of common standards to integrate structural, experimental  ...  They also thank Proteome Systems (Tyrian Diagnostics) for their release of GlycoSuiteDB to the public domain.  ... 
doi:10.1002/pmic.201100302 pmid:21898825 fatcat:oxz6sxorarcbbeqstqjocapnwu

Proteins will Fold Anyway!!

Indira Ghosh
2011 Journal of Biomolecular Structure and Dynamics  
In this connection it may be noted that the development of knowledgebased potentials is based on preferential interaction between amino acids, and the determination of protein structure by modeling and  ...  simulation, based on preferential contacts and interactions, has become very common (13-16 and references therein).  ...  In this connection it may be noted that the development of knowledgebased potentials is based on preferential interaction between amino acids, and the determination of protein structure by modeling and  ... 
doi:10.1080/073911011010524967 pmid:21142239 fatcat:rjnufmjtmbedffmp6qmnuhh6ee

Proteins will Fold Anyway!!

Indira Ghosh
2011 Journal of Biomolecular Structure and Dynamics  
In this connection it may be noted that the development of knowledgebased potentials is based on preferential interaction between amino acids, and the determination of protein structure by modeling and  ...  simulation, based on preferential contacts and interactions, has become very common (13-16 and references therein).  ...  In this connection it may be noted that the development of knowledgebased potentials is based on preferential interaction between amino acids, and the determination of protein structure by modeling and  ... 
doi:10.1080/07391102.2011.10524967 fatcat:jrqvozk3fbhl7acpesa53qamz4

Systems Biology Approach for Mapping TNFα-NFκB Mathematical Model to a Protein Interaction Map

Mahesh Visvanathan, Christian Baumgartner, Bernhard Tilg, Gerald Henry Lushington
2010 The Open Systems Biology Journal  
We investigated different mathematical models concerning signaling pathways and built a new pathway model for TNF -NF B signaling using an integrative analytical approach.  ...  This integrative approach consists of a knowledgebase, model designing/visualization and simulation environments.  ...  ACKNOWLEDGEMENT This project was supported by Award Number P20 RR016475 from the National Center for Research Resources.  ... 
doi:10.2174/1876392801003010001 fatcat:z5g5475q4nc53fohkwsweroo3a

Mining to find the lipid interaction networks involved in Ovarian Cancers

Rajaraman Kanagasabai, Kothandaraman Narasimhan, Hong-Sang Low, Wee Tiong Ang, Aaron Z Fernandis, Markus R Wenk, Mahesh A Choolani, Christopher J O Baker
2009 Summit on translational bioinformatics  
This information is discussed in a wide range of journals making it difficult for researchers to track the latest developments.  ...  We provide the first report on the roles and types of lipids involved in ovarian cancer based on the mining of literature and identify key lipid-protein interactions that may point to potential drug discovery  ...  Knowledgebase Population In its simplest form an OWL knowledgebase comprises of classes, instances of classes and properties (relations) linking instances.  ... 
pmid:21347172 pmcid:PMC3041567 fatcat:3bke7mgo7jhgziz5dq6yi7meom

The reactome pathway knowledgebase 2022

Marc Gillespie, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek Varusai (+23 others)
2021 Nucleic Acids Research  
The processes are annotated as an ordered network of molecular transformations in a single consistent data model.  ...  The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans  ...  The Reactome Knowledgebase is distinctive in focusing its manual annotation effort on a single species, Homo sapiens, and applying a single consistent data model across all domains of biology.  ... 
doi:10.1093/nar/gkab1028 pmid:34788843 pmcid:PMC8689983 fatcat:gszsloaqnffptgjwf32yaieq3q

A Guide to UniProt for Protein Scientists [chapter]

Claire O'Donovan, Rolf Apweiler
2010 Msphere  
One of the essential requirements of the proteomics community is a high quality annotated nonredundant protein sequence database with stable identifiers and an archival service to enable protein identification  ...  The scope of this chapter is to illustrate how Universal Protein Resource (UniProt) (The UniProt Consortium, Nucleic Acids Res. 38:D142-D148, 2010) can be best utilized for proteomics purposes with a particular  ...  The UniProt Knowledgebase (UniProtKB) (1) is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources.  ... 
doi:10.1007/978-1-60761-977-2_2 pmid:21082425 fatcat:a547fe36zfeq3f4csfvnrtjog4

The Universal Protein Resource (UniProt): an expanding universe of protein information

C. H. Wu
2006 Nucleic Acids Research  
A bibliography mapping service has been added, and an ID mapping service will be available soon. UniProt databases can be accessed online at  ...  The UniProt Knowledgebase (UniProtKB), comprising the manually annotated UniProtKB/Swiss-Prot section and the automatically annotated UniProtKB/ TrEMBL section, is the preeminent storehouse of protein  ...  PIR activities are also supported by the NIH grants for NIAID proteomic resource (HHSN266200400061C) and grid enablement (NCI-caBIG-ICR-10-10-01) and National Science Foundation grants for iProClass (DBI  ... 
doi:10.1093/nar/gkj161 pmid:16381842 pmcid:PMC1347523 fatcat:6xrpacost5entptndstyr7gnry

BioKC: a platform for quality controlled curation and annotation of systems biology models

Carlos Vega, Valentin Grouès, Marek Ostaszewski, Venkata Satagopam, Reinhard Schneider
2020 Zenodo  
Poster, slides, and video of the presentation of the talk BioKC: a platform for quality controlled curation and annotation of systems biology models during the workshop Biological network reconstruction  ...  Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research.[18] Kuperstein, I., Cohen, D. P., Pook, S., Viara, E., Calzone, L.  ...  NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.  ... 
doi:10.5281/zenodo.4033071 fatcat:yxmojuaebvbvnectyobojhlvcm

Workshop 3: Structural Genomics: A Discussion

2008 Biophysical Journal  
We use hydrosomes to confine and study transiently interacting molecular complexes on an individual basis.  ...  an enzyme family.  ... 
doi:10.1016/s0006-3495(08)79001-5 fatcat:yu3nrx3q3ng27o77sbux7owghy

The Universal Protein Resource (UniProt)

A. Bairoch
2004 Nucleic Acids Research  
Minor support for the EBIs involvement in UniProt comes from the two European Union contracts BioBabel (QLRT-2000-00981) and TEMBLOR (QLRI-2001-00015) and from the NIH grant 1R01HGO2273-01.  ...  Accordingly, UniProt acts as a central hub for biomolecular information with now more than four million cross-references to more than 60 databases.  ...  *To whom correspondence should be addressed: Tel: +44 0 1223 494435; Fax: +44 0 1223 494468; Email: apweiler@ebi.ac.uk The online version of this article has been published under an open access model.  ... 
doi:10.1093/nar/gki070 pmid:15608167 pmcid:PMC540024 fatcat:iqjosikdt5epfo6inmhb5uuiyy
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