Repository curation model organism genes interfaces databases protein. Medical search. Frequent questions

Secondary databases are:[clarification needed] 23andMe's database HapMap OMIM (Online Mendelian Inheritance in Man): inherited diseases RefSeq 1000 Genomes Project: launched in January 2008. (wikipedia.org)
These databases may hold many species genomes, or a single model organism genome. (wikipedia.org)
All SBML files in this directory were converted from KEGG (Kyoto Encyclopedia on Genes and Genomes) by using our conversion script kegg2sbml with the permission of Professor Minoru Kanehisa (Kyoto University). (systems-biology.org)
Moreover, genetic and simple obesity share similar structural and functional features of dysbiosis, such as higher production of toxins with known potential to induce metabolic deteriorations (e.g. trimethylamine-N-oxide and indoxyl sulphate), higher abundance of genomes containing genes coding enzymes involved in the production of these toxic co-metabolites and higher abundance of pathways for biosynthesis of bacterial antigens (such as endotoxin) [13-15]. (deepdyve.com)
In 1998, she and colleagues at other model organism databases (MODs) founded the Gene Ontology Consortium (GOC) as they recognized the need to create structured controlled vocabularies for molecular biology to allow comparison of data across different genomes and species. (biocuration.org)
Students will help develop tools and workﬂows to compile annotated libraries of genes and genomes, curate functional associations between genes and microbes in metabolism, and link microbial abundance to host gene/pathway expression and other outcomes. (bu.edu)
Typically, databases of related proteins focus on those from completely-sequenced genomes. (biomedcentral.com)
We have tested and established the best thresholds that allows a sequence to be selected as a correct member of a group, which allows the possibility of working with sequences from organisms with incompletely-sequenced genomes. (biomedcentral.com)
The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. (re3data.org)
With the completion of the human genome and the genomes of other species, we have a glimpse of many more genes than we ever had before to study. (pharmaceuticalintelligence.com)
SynteView allows a fast and easy visualization of conservation of gene adjacency in many prokaryotic genomes for which orthology and neighbourhood data have been computed and stored in SynteBase, a dedicated relational database. (molbiol-tools.ca)
BugView - is a genome browser for comparing the arrangement of genes on a pair of related genomes, and can also be used to view individual genomes. (molbiol-tools.ca)

Dr. Blake spent most of her career at the Jackson Laboratory (JAX) in Bar Harbor, Maine, where she was a Principal Investigator for the Mouse Genome Informatics project that includes the Mouse Genome Database for the laboratory mouse providing integrated genetic, genomic, and functional data for the study of human diseases. (biocuration.org)
The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. (re3data.org)
SSTAR , a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor - combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. (molbiol-tools.ca)
This tutorial shows how to use the UCSC genome browser to find a list of genes in a given genomic region. (incf.org)
In the example, data are extracted showing SNPs, genes, and phenotypes from a genomic region. (incf.org)

AuReMe enables the reconstruction of metabolic networks from different sources based on sequence annotation, orthology, gap-filling and manual curation. (irisa.fr)
4) The manual curation assistance PADmet module allows the reported metabolic networks and their metadata to be curated. (irisa.fr)
Clearly, manual curation and management of such "big" corpora are infeasible, and hence, the biomedical community has long been examining and making use of various kinds of Natural Language Processing (NLP) methods and techniques to, at least partially, facilitate their use. (biomedcentral.com)

Other databases Nucleosome positioning region database These databases collect genome sequences, annotate and analyze them, and provide public access. (wikipedia.org)
PANTHER Pathways consists of over 165, primarily signaling, pathways, each with subfamilies and protein sequences mapped to individual pathway components. (systems-biology.org)
Several approaches have been designed to cluster related sequences from different organisms into the same ortholog group. (biomedcentral.com)
Seed Linkage runs using as input a fasta formatted database and a MySQL [ 7 ] table that contains taxonomic information (obtained from NCBI Taxonomy database) for all sequences contained in the database. (biomedcentral.com)
CBS offers Comprehensive public databases of DNA- and protein sequences, macromolecular structure, g ene and protein expression levels, pathway organization and cell signalling, have been established to optimise scientific exploitation of the explosion of data within biology. (re3data.org)
The original protein sequence data prior to pre-processing, filtered protein sequences , and all outputs from NovelTree are available here . (arcadiascience.com)
The first step in reading life's record is determining which sets of gene sequences are related: we must find "gene families. (arcadiascience.com)
Sequence Manipulation Suite - is an incredible set of programs for manipulating DNA and protein sequences. (molbiol-tools.ca)

Rhea can be used for enzyme annotation, genome-scale metabolic modeling and omics-related analysis. (biokeanos.com)
Annotation of biomedical documents with machine intelligible semantics facilitates advanced, semantics-based text management, curation, indexing, and search. (biomedcentral.com)
metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. (hcmr.gr)

We describe a computational methodology allowing to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. (researchgate.net)
The Dupuis lab develops statistical approaches to identify specific genes or genetic variants that inﬂuence complex phenotypes through their associated quantitative traits, which are traits that can be measured numerically, such as height or blood pressure in humans, and seed size or oil content in plants. (bu.edu)

PomBase: the knowledgebase for the fission yeast Schizosaccharomyces pombe SubtiWiki: integrated database for the model bacterium Bacillus subtilis The primary databases make up the International Nucleotide Sequence Database (INSD). (wikipedia.org)
The include: DNA Data Bank of Japan (National Institute of Genetics) EMBL (European Bioinformatics Institute) GenBank (National Center for Biotechnology Information) DDBJ (Japan), GenBank (USA) and European Nucleotide Archive (Europe) are repositories for nucleotide sequence data from all organisms. (wikipedia.org)
These three databases are primary databases, as they house original sequence data. (wikipedia.org)
The information in this database is authored by biological researchers with expertise in their fields, maintained by the Reactome editorial staff, and cross-referenced with the sequence databases at NCBI , Ensembl and UniProt, the UCSC Genome Browser , HapMap, KEGG ( Gene and Compound), ChEBI , PubMed and GO . (systems-biology.org)
The output table reports the coverage of the protein structures aligned to the UniProt sequence, overcoming numbering differences in PDB structures and providing information regarding model quality, protein complexes, ligands, and nucleic acid chain binding. (bvsalud.org)
Choosing the right templates in the immunoglobulin superfamily (IgSF) is challenging because its members share low sequence identity and display a wide range of alternative binding sites despite structural homology.ResultsWe present a new approach to predict protein interfaces. (edu.in)
We have developed a method to cluster cognate proteins from multiple organisms beginning with only one sequence, through connectivity saturation with that Seed sequence. (biomedcentral.com)
However, a great part of the cognate proteins encoded by distinct proteomes is strictly similar, at the sequence level, to their counterparts in related species. (biomedcentral.com)
Here, we propose a methodology for finding highly-related groups of proteins to one single desired Seed sequence, classifying each of them as potential orthologs or in-paralogs into complete and or unfinished proteomes. (biomedcentral.com)
Using the access to the MySQL database the program automatically recognizes which sequence belongs to which organism, a procedure that facilitates the setup and limits BLAST searches to the set of interest (the ongoing hits). (biomedcentral.com)
Starting with protein sequence data, NovelTree outputs gene families, gene family trees, species trees, and genome-wide evolutionary dynamics. (arcadiascience.com)
As evolution tinkers, it leaves behind decodable signals in the form of gene sequence changes. (arcadiascience.com)
It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases locally stored. (molbiol-tools.ca)

Pathway diagrams are interactive and include tools for visualizing gene expression data in the context of the diagrams. (systems-biology.org)
REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. (biokeanos.com)
Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. (biokeanos.com)
Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. (biokeanos.com)
The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. (biokeanos.com)
The more than likely absence of known mechanistic and kinetic data for each of the individual proteins in a novel pathway hinders the process of translating network topology into a mathematical model. (biomedcentral.com)

The CellML.org model repository is part of the international Physiome Project, and is a resource containing hundreds of computational biology models encoded in the CellML format. (systems-biology.org)
human gut microbiome, data repositories, large-scale and integrative computational tools, modelling, immunomodulation, drug screening Background The human gastrointestinal tract is a complex ecosystem in which eukaryotic cells continuously interact with nutrients and with the complex microbial population of the gut microbiota [1]. (deepdyve.com)
In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. (researchgate.net)
The GOC is the primary resource for curation and standardization of functional information for all life forms, providing the ability to computational investigate molecular biology information. (biocuration.org)
Computational methods relying on protein structure strongly depend on the structure selected for investigation. (bvsalud.org)
Her research group is recognized as one of the country's leading computational groups in atomic-scale modeling of materials and algorithm development. (jhu.edu)
In addition to the computational research the center also has experimental efforts in gene expression analysis using DNA chips and data generation in relation to the physical and structural properties of DNA. (re3data.org)
To achieve such a goal, strategies that combine the different theoretical and computational methods to identify proteins and generate a set of plausible alternative network topologies for the process of interest are needed. (biomedcentral.com)

Human Protein Atlas (HPA): a public database with expression profiles of human protein coding genes both on mRNA and protein level in tissues, cells, subcellular compartments, and cancer tumors. (wikipedia.org)
Predicting tissue-specific mRNA and protein abundance in maize: A machine learning approach. (usda.gov)

Colonization of the gut starts just after birth when pioneering species interact, through surface receptors, with gut cells to promote the expression of a specific set of host genes and favour the colonization of commensal microorganisms [6]. (deepdyve.com)
Her background in evolutionary biology motivated her work to represent the relationships between genes across species whenever possible. (biocuration.org)
Key to this effort is the application of phylogenetic methods to identify conserved genes, map their evolutionary histories, reconstruct species relationships, and pinpoint when and where evolution has innovated the most. (arcadiascience.com)
Gene families are groups of genes found in multiple species that are derived from a common ancestor gene through duplications, and often have related functions. (arcadiascience.com)

Genes Genomics, 2020 Jun. (nih.gov)
Data Sharing and Ontology use among Agricultural Genetics, Genomics and Breeding Databases and Resources of the AgBioData Consortium. (usda.gov)
GrainGenes: A data-rich repository for small grains genetics and genomics. (usda.gov)
Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. (microbiologyresearch.org)

metadatabase is a database model for metadata management, global query of independent database, and distributed data processing. (wikipedia.org)
We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. (microbiologyresearch.org)
MetaboLights is a database for metabolomics studies, their raw experimental data and associated metadata. (biokeanos.com)
The Metabolomics Workbench serves as a national and international repository for metabolomics data and metadata and provides analysis tools and access to metabolite standards, protocols, tutorials, training, and more. (biokeanos.com)
Ohio State University launched openMDR (open metadata repository) in 2009, using local instances of LexEVS, BioPortal, and caDSR. (nih.gov)

The EMBL-EBI Complex Portal (www.ebi.ac.uk/intact/complex) is a central service that provides manually curated information on stable, on macromolecular complexes from model organisms. (stanford.edu)

EggNOG Database: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. (wikipedia.org)
Working with the Quest for Orthologs group, orthology specialists from Harvard's DIOPT group, and representatives from numerous MODs, she helped spearhead the development of the Alliance orthology resources that are essential for data integration across organisms. (biocuration.org)
Also, the repertoire of Cryptococcus neoformans may represent a better model fungal system within which to study the functions of the PPIases as its genome size and genetic tractability are equal to those of Saccharomyces cerevisiae , whilst its repertoires exhibits greater orthology to that of humans. (biomedcentral.com)

Due to the critical nature of research data resources, repositories, and datasets, the development of metrics to evaluate the usage, utility, and impact of a given repository is essential. (nih.gov)
The NIH then issued a report which presents the findings to better understand metrics currently used within the biomedical repository community, which can inform future NIH efforts to help develop this space and to understand patterns of use across datasets and repositories. (nih.gov)
These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. (microbiologyresearch.org)
The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications. (biokeanos.com)

Furthermore, the NIAID Data Ecosystem Discovery Portal developed by the National Institute of Allergy and Infectious Diseases (NIAID) enables searching across databases. (wikipedia.org)
Meta databases are databases of databases that collect data about data to generate new data. (wikipedia.org)
many are listed below Model organism databases provide in-depth biological data for intensively studied organisms. (wikipedia.org)
Curators also annotate the components of the models with terms from controlled vocabularies and links to other relevant data resources. (systems-biology.org)
An in-house algorithm predicts and ranks expert authors for each gene based on the data within FlyBase and extracts their email addresses from papers that we have curated. (stanford.edu)
We discuss the general utility of this approach for other databases that capture data from the research literature. (stanford.edu)
Web Application Programming Interfaces (APIs) are interfaces that data providers build to empower the outside world to interact with their business logic. (stanford.edu)
The data set is based on shared information from existing clinical databases-Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)-as well as population databases, all linked to a single point of access. (plos.org)
AskOmics is made of three software blocks: (1) a web interface for data import, allowing the creation of a local triplestore from user's datasheets and standard data, (2) an interactive web interface allowing 'à la carte' query-building, (3) a server performing interactions with local and distant triplestores (queries execution, management of users parameters). (irisa.fr)
Five modules are composing AuReMe: 1) The Model-management PADmet module allows manipulating and traceing all metabolic data via a local database. (irisa.fr)
Hence, EmbedSeg is fully open source (https://github.com/juglab/EmbedSeg), offering (i) tutorial notebooks to train EmbedSeg models and use them to segment object instances in new data, and (ii) a napari plugin that can also be used for training and segmentation without requiring any programming experience. (mpi-cbg.de)
The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed. (researchgate.net)
Harmonizing model organism data in the Alliance of Genome Resources. (biocuration.org)
We can use this model to discuss with our peers before we test the model in the laboratory or by comparison to available data. (biomedcentral.com)
Typical sources of protein structures include experimental structures available at the Protein Data Bank (PDB) and high-quality in silico model structures, such as those available at the AlphaFold Protein Structure Database. (bvsalud.org)
Moonlight uses gene expression as a primary data source and combines it with patterns related to cancer hallmarks and regulatory networks to identify oncogenic mediators. (bvsalud.org)
To better support a modern data resource ecosystem, NIH makes a distinction between data repositories and knowledgebases. (nih.gov)
While both are important for advancing biomedical research, data repositories and knowledgebases can have unique functions, metrics for success, and sustainability needs. (nih.gov)
Biomedical data repositories accept the submission of relevant data from the research community to store, organize, validate, archive, preserve, and distribute data in compliance with the FAIR Data Principles. (nih.gov)
Data repositories and knowledgebases exist on a spectrum of ability and readiness to adopt the desirable characteristics aligned with FAIR and TRUST principles. (nih.gov)
AbstractMotivationIncreasing efforts are being made in the field of machine learning to advance the learning of robust and accurate models from experimentally measured data and enable more efficient drug discovery processes. (edu.in)
IntAct provides a database system and analysis tools for molecular interaction data. (biokeanos.com)
The Human Metabolome Database (HMDB) is a database containing detailed information about small molecule metabolites found in the human body.It contains or links 1) chemical 2) clinical and 3) molecular biology/biochemistry data. (biokeanos.com)
VirHostNet 2.0 integrates an extensive and original literature-curated dataset of virus/virus and virus/host protein-protein interactions complemented with publicly available data. (biokeanos.com)
Additionally, an online database will be created to store and analyze the variant data. (bu.edu)
Students will gain knowledge in human genetic variability and DNA repeats, and skills in analyzing high-throughput sequencing data, algorithm design and testing, and database development. (bu.edu)
Options are available to focus on applied data study of neuronal gene expression, aquatic food-webs, or marine fishery management. (bu.edu)
This project involves developing statistical analyses which combine genome wide association results with prior information from "omics" studies (gene variant functionality, gene expression, methylation, metabolomic data, and proteomic data) to determine regions with common or rare genetic variants that are potentially causally associated with traits of interest. (bu.edu)
Note that the data content found in the IMSR is as supplied by strain repository holders. (re3data.org)
We was an download the dynamics of conflict in northern ireland power conflict and emancipation speech with 10 organisms who present indexes to find the position of our spatial 20th gauze( VE) to know investment data. (behindertesingles.de)
In this approach, mathematical models play a central role for the evaluation of the alternative network structures that arise from literature data-mining, phylogenetic profiling, structural methods, and human curation. (biomedcentral.com)
Increasing amounts of data that can be mined for information about how proteins in cells assemble as metabolic pathways, signal transduction pathways, and gene circuits, are generated each day. (biomedcentral.com)
Thus, it is a challenge to transform the network of interactions inferred from the analysis of static data into a causal network that allows for the creation of mathematical models whose dynamic behavior can be analyzed and tested against experimental observations. (biomedcentral.com)
The database)Wikipedia of dominant equipment in the inhibiting data is the immigration of severity must- that is played. (cdseidel.de)

The database currently holds approximately 2000 complexes with the majority from Saccharomyces cerevisiae, human and mouse. (stanford.edu)

Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. (researchgate.net)
MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. (biokeanos.com)

Mouse Genome Database (MGD): Knowledgebase for mouse- human comparative biology. (biocuration.org)
BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. (biokeanos.com)

But we have also at the same time glimpsed the finiteness of this list of genes, a disturbingly small list. (pharmaceuticalintelligence.com)

Some add curation of experimental literature to improve computed annotations. (wikipedia.org)
A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. (microbiologyresearch.org)
Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. (biomedcentral.com)
Using the Iron Sulfur cluster biogenesis in S. cerevisiae as a test case we indicate how this procedure can be used to analyze and validate the network model against experimental results. (biomedcentral.com)

Proteins derived from a common ancestor are termed homologs. (biomedcentral.com)

Generating clusters based only on individual proteins of interest is less time consuming than generating clusters for whole proteomes. (biomedcentral.com)

However, writing such summaries is a daunting task, given the number of genes in each organism (e.g. 13,929 protein coding genes in Drosophila melanogaster). (stanford.edu)
In FlyBase (the Drosophila genetics database) we have therefore developed a pipeline to obtain such summaries from researchers who have worked extensively on each gene. (stanford.edu)

2) The meneco python package allows the gaps of a metabolic network to be filled by using a topological approach that implements a logical programming approach to solve a combinatorial problem 3) The shogen python package allows genome and metabolic network to be aligned in order to identify genome units which contain a large density of genes coding for enzymes, it also implements a logical programming approach. (irisa.fr)
The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds. (biokeanos.com)
The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. (biokeanos.com)

The Reactome project is a collaboration among Cold Spring Harbor Laboratory , The European Bioinformatics Institute , and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. (systems-biology.org)
We recently proposed Moonlight as a bioinformatics framework to predict driver genes and analyze them in a system-biology-oriented manner based on -omics integration. (bvsalud.org)
Among these, we highlight those proposed by Sonnhammer and Koonin [ 1 ] which defines orthologs, in-paralogs and out-paralogs as subtypes of homolog protein/genes, which can be operationally used by bioinformatics tools. (biomedcentral.com)
The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. (biomedcentral.com)

Biological databases are stores of biological information. (wikipedia.org)
The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. (wikipedia.org)
Omics Discovery Index can be used to browse and search several biological databases. (wikipedia.org)
Database: The Journal of Biological Databases and Curation. (usda.gov)

For organisms that live in interaction altogether (microbiotas), complementarity between these networks can be exploited to predict cooperation events. (irisa.fr)
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. (researchgate.net)
We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. (researchgate.net)
There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. (researchgate.net)
This project will center on applying nonlinear causal inference to identify interaction between scales of complexity in natural systems (e.g. single fish populations and ecosystem functioning or single cell expression and organism physiology). (bu.edu)

The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. (plos.org)
The Gene Ontology Consortium. (biocuration.org)

This tutorial shows how to find all the single nucleotide polymorphisms (SNPs) upstream from genes using the UCSC Genome Browser. (incf.org)
This tutorial shows how to obtain coordinates of genes, then input those coordinates into the UCSC Genome Browser for display. (incf.org)

Tools for querying and downloading gene expression profiles are provided. (wikipedia.org)

Alanyl-tRNA synthetase 1 (AARS1) gene mutation in a family with intermediate Charcot-Marie-Tooth neuropathy. (nih.gov)
In addition, it can be used to predict genetic interactions [3] by comparing the sensitivity value of a double gene mutation from the value predicted from single mutations, and reveal the network intervention [4] by applying the state-flip mutation subject to a single gene. (researchgate.net)
Such a mechanistic indicator could be for example a mutation in the regulatory regions for the candidate gene. (bvsalud.org)
Those oncogenic mediators with at least one driver mutation are retained as the final set of driver genes. (bvsalud.org)
Could we accurately predict the phenotype of a nonle-thal mutation in these genes in a multicellular organ-ism? (pharmaceuticalintelligence.com)

A humanized yeast model reveals dominant-negative properties of neuropathy-associated alanyl-tRNA synthetase mutations. (nih.gov)

Although we can connect structure to the gene, we can no longer infer its larger purpose in the cell or in the organism. (pharmaceuticalintelligence.com)

The Database of Quantitative Cellular Signalling (DOQCS) is a repository of models of signalling pathways present in the neurons. (systems-biology.org)

Next, based on the similarity of residue level conservation scores derived from the evolutionary profiles, a query protein is hierarchically clustered with all available template proteins in its superfamily with known interface definitions. (edu.in)
There are different subtypes of homology relationships attributed to proteins based on an evolutionary point of view. (biomedcentral.com)

accordingly, many proteins are ignored by the currently available databases of cognate proteins, despite the high amount of important genes that are functionally described only for these incomplete proteomes. (biomedcentral.com)

It includes reaction schemes, concentrations, rate constants, as well as annotations on the models. (systems-biology.org)
It provides unique identifiers, names and synonyms, list of complex members with their unique identifiers (UniProt, ChEBI, RNAcentral), function, binding and stoichiometry annotations, descriptions of their topology, assembly structure, ligands and associated diseases as well as cross-references to the same complex in other databases (e.g. (stanford.edu)
On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. (biocuration.org)

More and more we come to realize that understanding the con-served genes and their conserved circuits will require an understanding of their special properties that allow them to function together to generate different pheno-types in different tissues of metazoan organisms. (pharmaceuticalintelligence.com)

https://web.cci.emory.edu/confluence/download/attachments/4033450/CCI-TR-2012-1.pdf]\] # Zheng S, Wang F, Lu J, Saltz J. *Enabling Ontology Based Semantic Queries in Biomedical Database Systems. (nih.gov)

This is reflected by the fact that 498 of the 968-residue polypeptide human AARS shares 41% identity witht the E.coli protein. (nih.gov)
Integration of Evidence across Human and Model Organism Studies: A Meeting Report. (neurotree.org)
Significant levels of human curation are traditionally required. (nih.gov)
This database, which predates caBIG®, provides curated information for animal models of human cancers. (nih.gov)
The tool operates on DNA templates for all organisms, and on human and mouse DNA/RNA. (incf.org)

Such networks can then be translated into mathematical models whose dynamic behavior can be analyzed and compared to that of the real system, thus discriminating against some of the proposed topologies when they do not reproduce the expected behavior. (biomedcentral.com)

Curation focuses on quality assurance and quality control. (nih.gov)

Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2 . (plos.org)
All generate variability in the protein repository present in one population. (biomedcentral.com)

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. (usda.gov)
Once the oncogenic mediators are identified, it is important to include extra levels of evidence, called mechanistic indicators, to identify driver genes and to link the observed gene expression changes to the underlying alteration that promotes them. (bvsalud.org)
Investigating astrocyte maturation in a cell culture model revealed that in vitro-differentiated astrocytes lack expression of many mature astrocyte-specific genes, including genes for the transcription factors Rorb, Dbx2, Lhx2 and Fezf2. (nature.com)
We show that astrocyte maturation is promoted by extrinsic signals that induce multiple transcription factors that act largely independently to regulate distinct gene expression modules that together promote a mature astrocytic phenotype. (nature.com)
The decreased expression and inhibition of nuclear transfer of GLI1 downregulated macrophage M1 polarization and osteoclast activation, the effect of which was achieved by modulation of DNA methyltransferases (DNMTs) via transcriptional regulation and protein interactions. (elifesciences.org)
The tools can perform powerful whole genome analyses such as prediction of replication origins and termini, estimation of gene expression from codon usage, and genome information visualization. (molbiol-tools.ca)

While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. (biomedcentral.com)
The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. (biomedcentral.com)
The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. (biomedcentral.com)

A component is usually a single protein in a given organism, but multiple proteins can sometimes play the same role. (systems-biology.org)
Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org . (plos.org)
Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org , to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. (plos.org)
It is highly relevant for the study of non-model organisms, or the comparison of metabolic networks for different strains or a single organism. (irisa.fr)
BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs. (biokeanos.com)

JWS Online is One of the first resources offering curation of the models it distributes, and online simulation. (systems-biology.org)
The feature labels in maps can be hyperlinked to external resources, allowing CGView maps to be integrated with existing web site content or databases. (molbiol-tools.ca)
Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. (rothamsted.ac.uk)

Prediction of driver genes (tumor suppressors and oncogenes) is an essential step in understanding cancer development and discovering potential novel treatments. (bvsalud.org)
Once clustered, a subset of the most closely related templates is selected, and an interface prediction is made. (edu.in)
The prediction of binding affinity is one of the most frequent tasks of compound bioactivity modelling. (edu.in)
Learned models for binding affinity prediction are assessed by their average performance on unseen samples, but point predictions are typically not provided with a rigorous confidence assessment. (edu.in)

Web-based kinetic modelling using JWS Online. (systems-biology.org)

The IMSR is a searchable online database of mouse strains, stocks, and mutant ES cell lines available worldwide, including inbred, mutant, and genetically engineered strains. (re3data.org)

The peptidyl-prolyl cis / trans isomerase (PPIase) class of proteins is traditionally comprised of three distinct protein families, the cyclophilins (cyclosporin A binding proteins), FKBPs (FK506 binding proteins) and parvulins, that are linked by their shared ability to catalyse the bond preceding a proline residue between its cis and trans forms. (biomedcentral.com)

You can find the NovelTree workflow in this GitHub repository . (arcadiascience.com)

Some fungi have been used as model systems to investigate the role of PPIases within the cell, however how representative these repertoires are of other fungi or humans has not been fully investigated. (biomedcentral.com)

The Cadbiom software provides a formal framework to help the modeling of biological systems such as cell signaling network with Guarder Transition Semantics. (irisa.fr)
Approaches such as the conformal predictor framework equip conventional models with a more rigorous assessment of confidence for individual point predictions. (edu.in)
This resource uses the IntAct database framework to help reduce the effort of scientists and improve on IT development. (biokeanos.com)

Publication of papers and other documents based on this database must include proper acknowledgment of this fact. (systems-biology.org)
Each model is carefully curated to verify that it corresponds to the reference publication and give the proper numerical results. (systems-biology.org)
Also considering the knowledge that did not make it to publication or that is stored in various types of databases and file systems, many scientists find it increasingly challenging to ensure that all potentially relevant facts are considered whilst forming a hypothesis. (biomedcentral.com)

Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. (biomedcentral.com)
Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. (biomedcentral.com)
Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. (biokeanos.com)
Critical evaluation of the obtained results through this procedure allows devising new wet lab experiments to confirm its predictions or provide alternative explanations for further improving the models. (biomedcentral.com)

Anatomy3

Organisms21

Diseases5

Chemicals and Drugs20

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Psychiatry and Psychology3

Phenomena and Processes62

Disciplines and Occupations18

Anthropology, Education, Sociology and Social Phenomena7

Technology, Industry, Agriculture6

Humanities2

Information Science83

Health Care30

Geographicals1

Genomes12

Genomic5

Manual curation3

Sequences8

Annotation3

Phenotypes2

Sequence13

Pathway6

Computational8

MRNA and protein2

Species4

Genomics4

Metadata5

Manually curated1

Orthology3

Datasets4

Data34

Complexes1

Experimentally2

Knowledgebase2

List of ge1

Experimental4

Derived from a common ancestor1

Individual proteins1

Drosophila2

Enzymes3

Bioinformatics4

Biological databases4

Interaction5

Consortium2

Genome Browser2

Downloading gene expression1

Mutation5

Yeast model1

Infer1

Pathways1

Evolutionary2

Functionally1

Annotations3

Tissues1

Ontology1

Human5

Behavior1

Focuses1

Generate2

Expression6

Methodology3

Single5

Resources3

Prediction4

Kinetic1

Strains1

Traditionally1

Workflow1

Fungi1

Framework3

Publication3

Experiments4