LitCovid-sentences | | | 5.63 M | | Jin-Dong Kim | 2023-11-24 | Developing | |
LitCovid-PD-CLO | | | 3.73 M | | Jin-Dong Kim | 2023-11-24 | Developing | |
LitCovid-PMC-OGER-BB | | Annotating PMC articles with OGER and BioBert, according to an hand-crafted Covid-specific dictionary and the 10 different CRAFT ontologies (http://bionlp-corpora.sourceforge.net/CRAFT/):
Chemical Entities of Biological Interest (CHEBI),
Cell Ontology (CL),
Entrez Gene (UBERON),
Gene Ontology (biological process (GO-BP), cellular component (GO-CC), and molecular function (GO-MF),
NCBI Taxonomy (NCBITaxon),
Protein Ontology (PR),
Sequence Ontology (SO) | 3.14 M | Fabio Rinaldi | Nico Colic | 2023-11-24 | Developing | |
PMID_GLOBAL | | Global sentencer tagging of public PMID abstracts.
Open and publicly available to the global community. | 2.24 M | | alo33 | 2023-11-24 | Developing | |
LitCovid-PD-CHEBI | | | 1.43 M | | Jin-Dong Kim | 2023-11-24 | Developing | |
Epistemic_Statements | | The goal of this work is to identify epistemic statements in the scientific literature. An epistemic statement is a statement of unknowns, hypotheses, speculations, uncertainties, including statements of claims, hypotheses, questions, explanations, future opportunities, surprises, issues, or concerns within a sentence. The unit of an epistemic statement is a sentence automatically parsed. The classification is binary - epistemic statement or not. We will label epistemic statements only and one can assume that if a statement is not labeled, then it is not an epistemic statement.
The classifier is a CRF, trained on gold standard annotations of epistemic statements that are currently ongoing. We report an F-measure of 0.91 after 5-fold cross validation on a test set with 914 statements and an F-measure of 0.9 on a held out document with 130 statements. This project is still under development and is submitted to be used for the CovidLit project and associated Hackathon.
Please contact Mayla if you have any questions. | 1.42 M | | mboguslav | 2023-11-24 | Developing | |
Biotea | | NCBO annotation on full text for PMC articles. Currently including only a small set of 2811 articles corresponding to those supporting curated diesease-protein annotation from UniProt and with machine-processable full text. | 894 K | L. Garcia | | 2023-11-24 | Developing | |
NCBITAXON | | annotation for NCBI taxonomy.
Automatic annotation by PD-NCBITaxon. | 502 K | | Jin-Dong Kim | 2023-11-24 | Developing | |
GlyCosmos6-Glycan-Motif-Structure | | Automatic annotation by Covid-19_Glycan-Motif. | 107 K | | Jin-Dong Kim | 2023-11-24 | Developing | |
GlyCosmos6-CLO | | Automatic annotation by PC-CLO. | 1.18 M | | Jin-Dong Kim | 2023-11-24 | Developing | |
GlyCosmos6-Glycan-Motif-Image | | | 87.8 K | | Jin-Dong Kim | 2023-11-24 | Developing | |
GlyCosmosP-Glycan-Motif | | | 8 | | Jin-Dong Kim | 2023-11-24 | Developing | |
tees-test | | Random PMC document used for testing during the development of a RESTful TEES parsing web service. | 3.39 K | Nico Colic | Nico Colic | 2023-11-24 | Developing | |
bionlp-ost-19-BB-rel-ner-test | | | 125 | | ldeleger | 2023-11-24 | Developing | |
genia-medco-coref | | Coreference annotation made to the Genia corpus, following the MUC annotation scheme. It is a product of the collaboration between the Genia and the MedCo projects. | 45.9 K | MedCo project & Genia project | Jin-Dong Kim | 2023-11-24 | Developing | |
Covid19_manual_annotation_v2 | | | 4.58 K | | AikoHIRAKI | 2023-11-24 | Developing | |
PubMed-German-test | | A collection of PubMed abstracts which are written in German | 0 | | Jin-Dong Kim | 2023-11-24 | Developing | |
PT_NER_NEL_Diana | | | 318 | | dpavot | 2023-11-24 | Developing | |
PubMed-2017 | | abstracts published in 2017. | 0 | | Jin-Dong Kim | 2023-11-24 | Developing | |
updated_tagging_age_PMA_annotations | | | 1.94 K | | laurenc | 2023-11-26 | Developing | |