ORGANISMS
ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.
Description
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ORGANISMS is a weekly updated web resource that facilitates taxonomy-aware search and retrieval of articles. To this end, the the resource performs named entity recognition of terms from the NCBI Taxonomy on PubMed abstracts. The resource further provides download files of organism-disease and organism-tissue associations extracted through automatic text mining.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
Webpage:
https://organisms.jensenlab.org/Webpage
More detailed information about this field from each metasource.
https://organisms.jensenlab.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:31:07.403080
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Name: CC-BY-4.0Licence name
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Publications:
Publications
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The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
PMID: 23823062
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
Publications
More detailed information about this field from each metasource.
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
PMID: 23823062
metasource: bio.tools
version: extracted_at: 2022-11-04T11:31:07.403080
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The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
PubMed citations: 48.
48 articles citing: The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text
PREGO: A Literature and Data-Mining Resource to Associate Microorganisms, Biological Processes, and Environment Types. PMID:35208748
Acronyms and Opportunities for Improving Deep Nets. PMID:34988434
ECO-CollecTF: A Corpus of Annotated Evidence-Based Assertions in Biomedical Manuscripts. PMID:34327299
Taxallnomy: an extension of NCBI Taxonomy that produces a hierarchically complete taxonomic tree. PMID:34325658
Biomedical and clinical English model packages for the Stanza Python NLP library. PMID:34157094
Exploring Noninvasive Biomarkers with the miRandola Database: A Tool for Translational Medicine. PMID:33835456
Human pathways in animal models: possibilities and limitations. PMID:33524155
Improving biomedical named entity recognition with syntactic information. PMID:33238875
TCRD and Pharos 2021: mining the human proteome for disease biology. PMID:33156327
DrugCentral 2021 supports drug discovery and repositioning. PMID:33151287
Recognition of Latin scientific names using artificial neural networks. PMID:32765977
Building a PubMed knowledge graph. PMID:32591513
On the hunt for the alternate host of Hemileia vastatrix. PMID:31871671
BioBERT: a pre-trained biomedical language representation model for biomedical text mining. PMID:31501885
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Exploring the dark genome: implications for precision medicine. PMID:31270560
CoCoScore: context-aware co-occurrence scoring for text mining applications using distant supervision. PMID:31199464
Solr-Plant: efficient extraction of plant names from text. PMID:31117932
Design, implementation, and operation of a rapid, robust named entity recognition web service. PMID:30850898
COPIOUS: A gold standard corpus of named entities towards extracting species occurrence from biodiversity literature. PMID:30700967
miRBase: from microRNA sequences to function. PMID:30423142
Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000. PMID:30265449
Viruses.STRING: A Virus-Host Protein-Protein Interaction Database. PMID:30249048
SPRENO: a BioC module for identifying organism terms in figure captions. PMID:29873706
Transfer learning for biomedical named entity recognition with neural networks. PMID:29868832
TISSUES 2.0: an integrative web resource on mammalian tissue expression. PMID:29617745
Unexplored therapeutic opportunities in the human genome. PMID:29472638
Entity recognition in the biomedical domain using a hybrid approach. PMID:29122011
miRandola 2017: a curated knowledge base of non-invasive biomarkers. PMID:29036351
Deep learning with word embeddings improves biomedical named entity recognition. PMID:28881963
A neural network multi-task learning approach to biomedical named entity recognition. PMID:28810903
Constructing a biodiversity terminological inventory. PMID:28414821
TIN-X: target importance and novelty explorer. PMID:28398460
RAIN: RNA-protein Association and Interaction Networks. PMID:28077569
A corpus for plant-chemical relationships in the biomedical domain. PMID:27650402
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. PMID:27589962
Overview of the interactive task in BioCreative V. PMID:27589961
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions. PMID:27465130
Extracting Characteristics of the Study Subjects from Full-Text Articles. PMID:26958181
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. PMID:26896844
The SIDER database of drugs and side effects. PMID:26481350
Comprehensive comparison of large-scale tissue expression datasets. PMID:26157623
ENVIRONMENTS and EOL: identification of Environment Ontology terms in text and the annotation of the Encyclopedia of Life. PMID:25619994
Morphological background detection and illumination normalization of text image with poor lighting. PMID:25426639
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
An analysis on the entity annotations in biological corpora. PMID:25254099
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. PMID:24573882
Protein-driven inference of miRNA-disease associations. PMID:24273243
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