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NameTDescription# Ann.AuthorMaintainerUpdated_atStatus

41-60 / 491 show all
craft-ca-core-dev Development data for CRAFT CA shared task, core concepts only. This project contains the development (training) annotations for the Concept Annotation task of the CRAFT Shared Task 2019. This particular set of concept annotations is the "core" set. See the task description for details, but this set contains only annotations to concepts that appear in the original 10 Open Biomedical Ontologies used for annotation. (That is to say, it does not contain any annotations to extension classes).59.8 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
craft-sa-dev Development data for CRAFT SA shared task. This project contains the development (training) annotations for the Structural Annotation task of the CRAFT Shared Task 2019. This particular set contains token and sentence annotations with tokens linked via dependency relations. These dependency relations were automatically generated using the manually curated CRAFT constituency treebank files as input.490 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
craft-ca-core-ex-dev Development data for CRAFT CA shared task, core concepts + EXTENSIONS. This project contains the development (training) annotations for the Concept Annotation task of the CRAFT Shared Task 2019. This particular set of concept annotations is the "core+extensions" set. See the task description for details, but this set contains annotations to concepts that appear in the original 10 Open Biomedical Ontologies used for annotation PLUS annotations to extension classes created using the core concepts.90.2 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
LitCovid-PD-FMA-UBERON-v1 PubDictionaries annotation for anatomy terms - updated at 2020-04-20 Disease term annotation based on FMA and Uberon. Version 2020-04-20. The terms in FMA and Uberon are loaded in PubDictionaries (FMA and Uberon), with which the annotations in this project are produced. The parameter configuration used for this project is here for FMA and there for Uberon. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.4.3 KJin-Dong Kim2020-11-20Released
LitCovid-PD-HP-v1 PubDictionaries annotation for human phenotype terms - updated at 2020-04-20 Disease term annotation based on HP. Version 2020-04-20. The terms in HP are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.3.03 KJin-Dong Kim2020-11-20Released
LitCovid-PD-MONDO-v1 PubDictionaries annotation for disease terms - updated at 2020-04-20 It is based on MONDO Version 2020-04-20. The terms in MONDO are loaded in PubDictionaries, with which the annotations in this project are produced. The parameter configuration used for this project is here. Note that it is an automatically generated dictionary-based annotation. It will be updated periodically, as the documents are increased, and the dictionary is improved.13.4 KJin-Dong Kim2020-11-20Released
RELISH-DB Abstracts contained in the data of the RELISH-DB (https://relishdb.ict.griffith.edu.au) made available for download here. Data was downloaded from here: https://figshare.com/projects/RELISH-DB/60095 Related publication: https://academic.oup.com/database/article/doi/10.1093/database/baz085/5608006#20072202302020-12-03Released
LitCovid-v1-docs A comprehensive literature resource on the subject of Covid-19 is collected by NCBI: https://www.ncbi.nlm.nih.gov/research/coronavirus/ The LitCovid project@PubAnnotation is a collection of the titles and abstracts of the LitCovid dataset, for the people who want to perform text mining analysis. Please note that if you produce some annotation to the documents in this project, and contribute the annotation back to PubAnnotation, it will become publicly available together with contribution from other people. If you want to contribute your annotation to PubAnnotation, please refer to the documentation page: http://www.pubannotation.org/docs/submit-annotation/ The list of the PMID is sourced from here The 6 entries of the following PMIDs could not be included because they were not available from PubMed:32161394, 32104909, 32090470, 32076224, 32161394 32188956, 32238946. Below is a notice from the original LitCovid dataset: PUBLIC DOMAIN NOTICE National Center for Biotechnology Information This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. Although all reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. Please cite the authors in any work or product based on this material : Chen Q, Allot A, & Lu Z. (2020) Keep up with the latest coronavirus research, Nature 579:193 0Jin-Dong Kim2020-12-22Released
LitCovid-sentences-v1 Sentence segmentation of all the texts in the LitCovid literature. The segmentation is automatically obtained using the TextSentencer annotation service developed and maintained by DBCLS.16.5 KJin-Dong Kim2021-01-17Released
AGAC_test AGAC track test set in BioNLP-OST 2019, Hong Kong0xiajingbo2021-01-19Released
AGAC_training AGAC track training set in BioNLP-OST 2019, Hong Kong3.32 Kxiajingbo2021-01-19Released
AGAC_sample AGAC track samples in BioNLP-OST 2019, Hong Kong874xiajingbo2021-01-19Released
c_corpus Documents included in the c_corpus: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv107 K2021-01-27Released
bionlp-st-epi-2011-training The training dataset from the Epigenetics and Post-translational Modifications (EPI) task in the BioNLP Shared Task 2011. The core entities of the task are genes and gene products (RNA and proteins), identified in the data simply as "Protein" annotations. 7.59 KGENIAYue Wang2021-03-10Released
bionlp-st-cg-2013-training The training dataset from the cancer genetics task in the BioNLP Shared Task 2013. Composed of anatomical and molecular entities.10.9 KNaCTeMYue Wang2021-03-10Released
bionlp-st-bb3-2016-training Entity (bacteria, habitats and geographical places) annotation to the training dataset of the BioNLP-ST 2016 BB task. For more information, please refer to bionlp-st-bb3-2016-development and bionlp-st-bb3-2016-test. Bacteria Bacteria entities are annotated as contiguous spans of text that contains a full unambiguous prokaryote taxon name, the type label is Bacteria. The Bacteria type is a taxon, at any taxonomic level from phylum (Eubacteria) to strain. The category that the text entities have to be assigned to is the most specific and unique category of the NCBI taxonomy resource. In case a given strain, or a group of strains is not referenced by NCBI, it is assigned with the closest taxid in the taxonomy. Habitat Habitat entities are annotated as spans of text that contains a complete mention of a potential habitat for bacteria, the type label is Habitat. Habitat entities are assigned one or several concepts from the habitat subpart of the OntoBiotope ontology. The assigned concepts are as specific as possible. OntoBiotope defines most relevant microorganism habitats from all areas considered by microbial ecology (hosts, natural environment, anthropized environments, food, medical, etc.). Habitat entities are rarely referential entities, they are usually noun phrases including properties and modifiers. There are rare cases of habitats referred with adjectives or verbs. The spans are generally contiguous but some of them are discontinuous in order to cope with conjunctions. Geographical Geographical entities are geographical and organization places denoted by official names.1.28 KINRAYue Wang2021-03-10Released
BioLarkPubmedHPO 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference standard for free text annotation of human phenotypes. For more info, please see Groza et al. "Automatic concept recognition using the human phenotype ontology reference and test suite corpora", 2015.7.16 KTudor Grozasimon2021-03-10Released
AnEM_abstracts 250 documents selected randomly from citation abstracts Entity types: organism subdivision, anatomical system, organ, multi-tissue structure, tissue, cell, developing anatomical structure, cellular component, organism substance, immaterial anatomical entity and pathological formation Together with AnEM_full-texts, it is probably the largest manually annotated corpus on anatomical entities.1.91 KNaCTeMYue Wang2021-03-10Released
PennBioIE The PennBioIE corpus (0.9) covers two domains of biomedical knowledge. One is the inhibition of the cytochrome P450 family of enzymes (CYP450 or CYP for short) , and the other domain is the molecular genetics of dance (oncology or onco for short).23.8 KUPenn Biomedical Information Extraction ProjectYue Wang2021-03-10Released
PubMed_Structured_Abstracts Sections (zones) as retrieved from PubMed.131 Kzebet2021-03-10Released
NameT# Ann.AuthorMaintainerUpdated_atStatus

41-60 / 491 show all
craft-ca-core-dev 59.8 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
craft-sa-dev 490 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
craft-ca-core-ex-dev 90.2 KUniversity of Colorado Anschutz Medical Campuscraft-st2020-10-02Released
LitCovid-PD-FMA-UBERON-v1 4.3 KJin-Dong Kim2020-11-20Released
LitCovid-PD-HP-v1 3.03 KJin-Dong Kim2020-11-20Released
LitCovid-PD-MONDO-v1 13.4 KJin-Dong Kim2020-11-20Released
RELISH-DB 02020-12-03Released
LitCovid-v1-docs 0Jin-Dong Kim2020-12-22Released
LitCovid-sentences-v1 16.5 KJin-Dong Kim2021-01-17Released
AGAC_test 0xiajingbo2021-01-19Released
AGAC_training 3.32 Kxiajingbo2021-01-19Released
AGAC_sample 874xiajingbo2021-01-19Released
c_corpus 107 K2021-01-27Released
bionlp-st-epi-2011-training 7.59 KGENIAYue Wang2021-03-10Released
bionlp-st-cg-2013-training 10.9 KNaCTeMYue Wang2021-03-10Released
bionlp-st-bb3-2016-training 1.28 KINRAYue Wang2021-03-10Released
BioLarkPubmedHPO 7.16 KTudor Grozasimon2021-03-10Released
AnEM_abstracts 1.91 KNaCTeMYue Wang2021-03-10Released
PennBioIE 23.8 KUPenn Biomedical Information Extraction ProjectYue Wang2021-03-10Released
PubMed_Structured_Abstracts 131 Kzebet2021-03-10Released