*  Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into...
... patens protein-coding genes in order for it to serve as a reference model organism and plant "flagship". With the development ... DL and ADZ conceived, supervised and designed the curation process, annotation interfaces and database backends. KB implemented ... Model organism databases (MODs, e.g. Gramene [33], TAIR [34], FlyBase [35]) are integrated, web-accessible resources, which are ... patens protein-coding genes to unravel its full potential as a reference model organism. To facilitate such efforts we ...
  https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-498
*  The Seven Deadly Sins of Bioinformatics
Yet another database … ,ul,,li,Organism databases ,/li,,/ul,,ul,,li,Counter example ,/li,,/ul,,ul,,ul,,li,Generic Model ... li,,/ul,,/ul,,ul,,ul,,li,protein identifications using Mascot scores. ,/li,,/ul,,/ul,,ul,,ul,,li,differentially expressed genes ... maintain legacy interfaces until clients can port their scripts ,/li,,/ul,,ul,,li,Support as many interfaces as you can ,/li,,/ ... Cameron's 5 th Commandment of Curation ,/li,,/ul,,ul,,li,Exceptionalism paralysis. ,/li,,/ul,,ul,,li,Gather requirements ...
  https://www.slideshare.net/dullhunk/the-seven-deadly-sins-of-bioinformatics/
*  List of biological databases - Wikipedia
Xenbase, genome of the model organism Xenopus tropicalis and Xenopus laevis Wormbase, genome of the model organism ... Protein Model Portal (PMP) Meta database that combines several databases of protein structure models (Biozentrum, Basel, ... Some add curation of experimental literature to improve computed annotations. These databases may hold many species genomes, or ... and exon sequencing of at least 1,200 genes. TDR Targets A chemogenomics database focused on drug discovery in tropical ...
  https://en.wikipedia.org/wiki/List_of_biological_databases
*  Toward an interactive article: integrating journals and biological databases | BMC Bioinformatics | Full Text
We are planning on linking articles from more model organisms and are looking for other databases and journals to actively ... ambiguities across databases may occur in C. elegans papers; for example, HID-1 is the name of a protein in C. elegans and in ... Finally, ongoing curation at the biological database ensures that linked content evolves with the field. This linking has ... Finally, several of these tools are limited in scope to a minimum number of entity types e.g., genes, proteins, or chemicals; ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-175
*  PaperBLAST: Text Mining Papers for Information about Homologs | mSystems
This works well for non-model organisms, but some articles about proteins from model organisms are missed. The incorporation of ... Unfortunately, the databases of protein function that are used to make annotations are far from complete. As an example, the ... As an alternative to expert curation, text-mining tools can find scientific articles that discuss a protein of interest (see, i ... Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins ...
  https://msystems.asm.org/content/2/4/e00039-17
*  Linking genes to literature: text mining, information extraction, and retrieval applications for biology | Genome Biology |...
Model Organism databases; OBO, Open Biomedical Ontologies; RGD, Rat Genome Database; SGD, Saccharomyces Genome Database; TAIR, ... and the PubGene system generates a graphical protein interaction network based on protein-protein literature co-occurrences [66 ... Manual curation is not sufficient for annotation of genomic databases. Bioinformatics. 2007, 23: i41-i48.PubMedPubMed Central ... of scholarly and scientific literature databases can be accessed online through search engines with simple query interfaces ...
  https://genomebiology.biomedcentral.com/articles/10.1186/gb-2008-9-s2-s8
*  MetNet Online: a novel integrated resource for plant systems biology | BMC Bioinformatics | Full Text
... obtained via manual curation and/or information from external databases) overlays the pathways. Third, a protein-protein ... MetNetDB uses a labelled graph model to represent biological networks and complex internal relationships. In this data model, ... he looks for pathways that are over-represented among the differentially expressed genes. Because numerous genes (thousands) ... The literature tab interfaces with PubMed to retrieve a current literature feed, in which the name of the pathway selected by ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-267
*  The ChEMBL-og: ADME SARfari: A tool for predicting and comparing cross-species ADME targets
... as model organism studies are the primary source of such data. For example, in an animal model study, which may be carried out ... The Human Protein Atlas - Protein expression data for human ADME Targets.. *ENSEMBL - Orthologue (using the Compara Service) ... PharmaADME - An online resource providing a list ADME related human genes. We used this to build our primary list of ADME ... system is called ADME SARfari and it aims to centralise all ADME data currently stored in ChEMBL and other related databases, ...
  https://chembl.blogspot.com/2014/01/adme-sarfari-tool-for-predicting-and_13.html
*  Comparative genome databases - OMICtools
Common features of two organisms will often be encoded within the DNA that is conserved between the species. More precisely, ... Likewise, the DNA sequences controlling the expression of genes that are regulated similarly in two related species should also ... It is the smallest known vertebrate genome, roughly 340 million base pairs, and has been selected as a model organism for ... Our recent updates in LegumeIP 2.0 include gene and protein sequences, gene models and annotations, syntenic regions, protein ...
  https://omictools.com/comparative-genome-data-category
*  Gene regulatory network - Wikipedia
By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, ... To speed up the manual curation of GRNs, some recent efforts try to use text mining, curated databases, network inference from ... This model is formally closer to a higher order recurrent neural network. The same model has also been used to mimic the ... In single-celled organisms, regulatory networks respond to the external environment, optimising the cell at a given time for ...
  https://en.wikipedia.org/wiki/Gene_regulatory_network
*  Gene Report for G00001823 - Genes2Cognition Neuroscience Research Programme
Systematic mapping of protein-protein interactions, or 'interactome' mapping, was initiated in model organisms, starting with ... Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones.. Nakajima D, Okazaki N, ... LIM domains also function as protein-binding interfaces, mediating specific protein-protein interactions. Limatin is a novel ... of the sequences indicated that 29 genes contained sequences with similarities to reported genes in the GenBank/EMBL databases ...
  http://www.genes2cognition.org/db/Gene/G00001823
*  Download The Small Church At Large: Thinking Local In A Global Context (Convergence Series) 2003
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*  ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses | BMC Bioinformatics | Full...
... adapting wikipedia principles to a model organism database. Nucleic Acids Research 2007, 35: D422-D426.PubMed CentralView ... Manual curation is not sufficient for annotation of genomic databases. Bioinformatics 2007, 23: 141-148.View ArticleGoogle ... Usability of existing repository interfaces. Designing easy-to-use and clean interfaces to assist data providers and data ... All of the methods discussed in this section are readily transferable from cDNA microarrays to tissue, protein, and ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-S6-S18
*  Primer on the Gene Ontology | SpringerLink
2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database:bar068Google ... which associate genes or gene products with terms from the Gene Ontology. Combining information from all organisms in one ... A wealth of tools-web-based services, stand-alone software, and programing interfaces-has been developed for applying the GO to ... The GO Consortium consists of a number of large databases working together to define standardised ontologies and provide ...
  https://link.springer.com/protocol/10.1007/978-1-4939-3743-1_3
*  Herman Skolnik Award Symposium 2016
... to develop quantitative metabolic models for model organisms, and to relate organism metabolic pathways within the context of ... Evan Bolton has referred to the proliferation of errors in public and private databases as "robochemistry". Manual curation of ... The first concerned MDM2 (mouse double minute 2 homologue), a protein that in humans is encoded by the MDM2 gene. The key ... Through better interfaces, terminology, metadata practices, and analytics, CEDAR optimizes the metadata pathway from provider ...
  http://bulletin.acscinf.org/book/export/html/909
*  List of Accepted Software Demos
... protein complexes and genes, all this linked to organism (including strains) and to biochemical reactions (in the case of ... Sequence annotation using diversity of databases. -Manual curation.. -Modulation of annotation intensity and diversity. - ... Goldman N,Yang Z (1994)A codon-based model of nucleotide substitution for protein-coding DNA sequences.Mol Biol Evol 11:725-36 ... REST interfaces for automated database queries, novel functionality for the gene expression warehouse and advanced data ...
  http://www.eccb06.org/new_pages/program/accepted_sw.html
*  SciLite Annotations
Manual curation is vital for maintaining quality information in biological databases. However, with the exponential growth in ... In the example below, an interactive Protein Data Bank (PDB) structure model is also provided when you click on a highlighted ... SciLite annotations enable biological terms and concepts, such as genes/proteins, diseases, organisms and accession numbers, to ... supports database curation processes, by highlighting biological concepts, making it easier to find key concepts described in ...
  http://pubtechgator.bmj.com/2016/09/scilite-annotations/
*  Mike Cherry | Stanford Medicine Profiles
The Model Organism BLASTP Best Hits resource displays, for each S.cerevisiae protein, the single most similar protein from ... Curated protein information in the Saccharomyces genome database DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION ... Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes ... The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces ...
  https://med.stanford.edu/profiles/j-michael-cherry
*  MicrobesOnline - Wikipedia
Kyoto Encyclopedia of Genes and Genomes (KEGG): a large collection of databases of genes, genomes, biological pathways, ... The single-genome data view can also show a protein-protein interaction browser that allows the inspection of interaction ... "Select Organism(s) to Display" box. The locus information can be viewed through the "view genes" option, and this gene can be ... Integrated Microbial Genomes System (IMG) BLAST BLAT (bioinformatics) FASTA format Gene ontology Hidden Markov model (HMM) ...
  https://en.wikipedia.org/wiki/MicrobesOnline
*  Resources and tools for the high-throughput, multi-omic study of intestinal microbiota, Briefings in Bioinformatics | 10.1093...
... or translated protein database searches [30]. That is, the assignment may be based on full protein-coding genes (CDSs) by means ... in the curation of the information contained in databases and other public biomolecule repositories. We sincerely believe that ... The steady-state compartmentalized approach models each organism in the microbial community as a single constraint-based model ... Last but not least, there is a general lack of graphical user interfaces to use many of the tools. This lack limits access of ...
  https://www.deepdyve.com/lp/ou_press/resources-and-tools-for-the-high-throughput-multi-omic-study-of-QU4byFWU0i
*  Philosophy of Systems and Synthetic Biology (Stanford Encyclopedia of Philosophy)
The human parasite Mycoplasma genitalium has been considered a model organism for the exploration of such questions due to its ... Omics fields allowed for large-scale measurements of co-expression between vast number of genes or associated protein ... 2002). Numerous databases, bio-ontologies, and software tools have been developed, emphasizing the ideals of Open Data and ... Since the call for standardization may be compromised by context-dependencies of data production and use, data-curation and the ...
  https://plato.stanford.edu/entries/systems-synthetic-biology/
*  Download Computational Statistics 2009
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*  Publications | bioontology.org
By contrast, model organism studies have been enhanced by ontologies shared among genomic databases. Here, we suggest that ... generation from gene or protein lists using ontological concepts present in manually curated text that describes those genes ... and distilling them down into structured knowledge that can be stored in databases as well as knowledgebases is called curation ... Although tag clouds are frequently available in web interfaces, they are typically used for providing an overview of key terms ...
  https://www.bioontology.org/publications
*  Download International Tables For Crystallography, Vol.d: Physical Properties Of Crystals(527) 2003
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*  Download A Brief Stop On The Road From Auschwitz 2015
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