disease_gene_microbe_small | | Small version (48 abstract that mention both Crohns and S. aureus) for development purposes
Abbreviation: dgm Content: annotated abstracts on Crohn’s disease or on on Staphylococcus aureus (according to the jensenlab.org indexing resources) Entity types: (three for a start, organisms (NCBI Taxonomy taxa), disease (Disease Ontology terms), human genes (ENSEMBL proteins) Aim: Explore indirect associations of diseases to microbial species in this corpus via gene co-mentions | 536 | | evangelos | 2023-11-27 | Testing | |
dailymed_spl | | Annotation of indications from DailyMed structured product labels | 0 | | micheldumontier | 2023-11-29 | Developing | |
CyanoBase | | Cyanobacteria are prokaryotic organisms that have served as important model organisms for studying oxygenic photosynthesis and have played a significant role in the Earthfs history as primary producers of atmospheric oxygen.
Publication: http://www.aclweb.org/anthology/W12-2430 | 1.1 K | Kazusa DNA Research Institute and Database Center for Life Science (DBCLS) | Yue Wang | 2023-11-26 | Released | |
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 K | University of Colorado Anschutz Medical Campus | craft-st | 2023-11-29 | Released | |
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 K | University of Colorado Anschutz Medical Campus | craft-st | 2023-11-29 | Released | |
Covid19_manual_annotation | | | 5.1 K | | AikoHIRAKI | 2023-11-29 | Developing | |
CORD-19_HIRAKI | | HIRAKI Annotation for CORD-19 | 2.98 K | | AikoHIRAKI | 2023-11-29 | Testing | |
consensus_PMA_Age_Indications | | | 1.7 K | | laurenc | 2023-11-28 | Beta | |
Computational_Biology | | | 0 | | Sophie Nam | 2023-11-29 | | |
CoMAGC | | In order to access the large amount of information in biomedical literature about genes implicated in various cancers both efficiently and accurately, the aid of text mining (TM) systems is invaluable. Current TM systems do target either gene-cancer relations or biological processes involving genes and cancers, but the former type produces information not comprehensive enough to explain how a gene affects a cancer, and the latter does not provide a concise summary of gene-cancer relations. In order to support the development of TM systems that are specifically targeting gene-cancer relations but are still able to capture complex information in biomedical sentences, we publish CoMAGC, a corpus with multi- faceted annotations of gene-cancer relations. In CoMAGC, a piece of annotation is composed of four semantically orthogonal concepts that together express 1) how a gene changes, 2) how a cancer changes and 3) the causality between the gene and the cancer. The multi-faceted annotations are shown to have high inter-annotator agreement. In addition, the annotations in CoMAGC allow us to infer the prospective roles of genes in cancers and to classify the genes into three classes according to the inferred roles. We encode the mapping between multi-faceted annotations and gene classes into 10 inference rules. The inference rules produce results with high accuracy as measured against human annotations. CoMAGC consists of 821 sentences on prostate, breast and ovarian cancers. Currently, the corpus deals with changes in gene expression levels among other types of gene changes. | 1.53 K | Lee et al | Hee-Jin Lee | 2023-11-24 | Released | |
Colil | | Colil (Comments on Literature in Literature) is a search service for citation contexts utilized in the biomedical domain. Colil searches for a cited paper in the Colil database and then returns a list of the citation contexts for it and its relevant papers based on co-citations. | 3.34 K | DBCLS | Toyofumi Fujiwara | 2023-11-28 | Testing | |
CoGe_Citation_Annotations | | Annotated PMC abstracts+full articles, that cite the "CoGe" papers (PMID: 18952863, 18269575).
Total Num Citations: 165
Total Num Unique Citations: 141
Total Num Abstracts: 165
Total Num Whole Articles: 165 | 0 | Heather Lent | hclent | 2023-11-29 | Uploading | |
CHEMDNER-training-test | | The training subset of the CHEMDNER corpus | 29.4 K | Martin Krallinger et al. | Jin-Dong Kim | 2023-11-27 | Testing | |
CellFinder | | CellFinder corpus | 4.75 K | Mariana Neves, Alexander Damaschun, Andreas Kurtz, Ulf Leser | Mariana Neves | 2023-11-27 | Released | |
c_corpus | | Documents included in the c_corpus: https://github.com/SMAFIRA/c_corpus/blob/master/SMAFIRAc_0.4_Annotations.csv | 107 K | | | 2023-11-29 | Released | |
cancer_precision | | for gene mutaiton and cancer therapy | 8 | | serenity | 2023-11-29 | Testing | |
Briefings | | | 0 | | Sophie Nam | 2023-11-29 | | |
blah6_medical_device | | BLAH6 hackathon project to annotate medical device indications in premarket approval statement summaries. The documents in this project serve as a corpus of premarket approval (PMA) statements that have undergone quality control. In particular, we have (1) removed non-ascii characters, (2) fixed some text segmentation errors, and (3) fixed some capitalization errors. | 0 | Stefano Rensi | therightstef | 2023-11-29 | Beta | |
blah6 | | device Annotator | 374 | | slee7268 | 2023-11-28 | Testing | |
BLAH2021-glytoucan-iupac | | | 0 | | kiyoko | 2021-01-19 | | |