Potentially relevant papers ranked for curation

[github-actions[bot]]

This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: (1) as a new prefix for a resource that can be added to the Bioregistry, (2) as a provider for an existing prefix, or (3) as a new publication for an existing prefix already in the Bioregistry.

These curations can happen in separate issues and pull requests. The full list of ranked papers can be found here. If you review any of these papers for relevance, you should edit the curated papers file here; these curations are taken into account when retraining the ranking model.

Entries for a batch of papers from 2022:

PubMed ID	Title
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39074139	FURNA: A database for functional annotations of RNA structures.
39014503	CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.
39047988	Knowledge infrastructure for integrated data management and analysis supporting new approach methods in predictive toxicology and risk assessment.
39115390	GENEVIC: GENetic data exploration and visualization via intelli- gent interactive console.
38991851	PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
38991828	isolateR: an R package for generating microbial libraries from Sanger sequencing data.
39049520	Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance.
39084442	HSADab: A comprehensive database for human serum albumin.
39104826	Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
39050757	Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
39064021	Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.
39028894	FragHub: A Mass Spectral Library Data Integration Workflow.
39044201	The Digital Atlas of Ancient Rare Diseases (DAARD) and its relevance for current research.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
39119155	Data Policy Finder: an easily integratable tool connecting data librarians with researchers to navigate publication requirements.
39005357	Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.
39044130	Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.
39010878	MotifbreakR v2: extended capability and database integration.

[github-actions[bot]]

This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: (1) as a new prefix for a resource that can be added to the Bioregistry, (2) as a provider for an existing prefix, or (3) as a new publication for an existing prefix already in the Bioregistry.

These curations can happen in separate issues and pull requests. The full list of ranked papers can be found here. If you review any of these papers for relevance, you should edit the curated papers file here; these curations are taken into account when retraining the ranking model.

New entries for 2024-07-10 to 2024-08-09:

PubMed ID	Title
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39074139	FURNA: A database for functional annotations of RNA structures.
39047988	Knowledge infrastructure for integrated data management and analysis supporting new approach methods in predictive toxicology and risk assessment.
39014503	CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.
39115390	GENEVIC: GENetic data exploration and visualization via intelli- gent interactive console.
38991851	PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
38991828	isolateR: an R package for generating microbial libraries from Sanger sequencing data.
39049520	Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance.
39084442	HSADab: A comprehensive database for human serum albumin.
39050757	Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
39064021	Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.
39044201	The Digital Atlas of Ancient Rare Diseases (DAARD) and its relevance for current research.
39028894	FragHub: A Mass Spectral Library Data Integration Workflow.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
39005357	Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.
39024225	Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.
39113691	CHHM: a Manually Curated Catalogue of Human Histone Modifications Revealing Hotspot Regions and Unique Distribution Patterns.
39044130	Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.
39101486	Transcriptomics and epigenetic data integration learning module on Google Cloud.

[github-actions[bot]]

This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: (1) as a new prefix for a resource that can be added to the Bioregistry, (2) as a provider for an existing prefix, or (3) as a new publication for an existing prefix already in the Bioregistry.

These curations can happen in separate issues and pull requests. The full list of ranked papers can be found here. If you review any of these papers for relevance, you should edit the curated papers file here; these curations are taken into account when retraining the ranking model.

New entries for 2024-08-02 to 2024-09-01:

PubMed ID	Title
39163546	GMMID: genetically modified mice information database.
39134728	Glycoscience data content in the NCBI Glycans and PubChem.
39145441	Clustering protein functional families at large scale with hierarchical approaches.
39212696	Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures.
39137905	Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39126204	The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop.
39174566	An ontology-based knowledge graph for representing interactions involving RNA molecules.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
39115390	GENEVIC: GENetic data exploration and visualization via intelli- gent interactive console.
39201310	Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations.
39143381	Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals.
39192607	Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms.
39184336	RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens.
39104826	Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
39171834	Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold.
39176907	Merging Biomedical Ontologies with BioSTransformers.
39101486	Transcriptomics and epigenetic data integration learning module on Google Cloud.
39213392	CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.

[github-actions[bot]]

This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways: (1) as a new prefix for a resource that can be added to the Bioregistry, (2) as a provider for an existing prefix, or (3) as a new publication for an existing prefix already in the Bioregistry.

These curations can happen in separate issues and pull requests. The full list of ranked papers can be found here. If you review any of these papers for relevance, you should edit the curated papers file here; these curations are taken into account when retraining the ranking model.

New entries for 2024-09-01 to 2024-10-01:

PubMed ID	Title
39229008	Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.
39294369	Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures.
39227781	Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants.
39241109	Interactive tools for functional annotation of bacterial genomes.
39230707	GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation.
39237205	CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes.
39339901	Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research.
39268315	OnetoMap Meta-Data: Healthcare Analytics Through Research.
39345624	Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements.
39212696	Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures.
39228707	Leveraging Generative AI to Accelerate Biocuration of Medical Actions for Rare Disease.
39235746	A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens.
39215721	AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function.
39282297	Genome-Wide Mapping of RNA-Protein Associations via Sequencing.
39341994	DRCTdb: disease-related cell type analysis to decode cell type effect and underlying regulatory mechanisms.
39201310	Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations.
39341795	SCancerRNA: Expression at the Single-cell Level and Interaction Resource of Non-coding RNA Biomarkers for Cancers.
39279874	BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.
39233898	Improving protein function prediction by learning and integrating representations of protein sequences and function labels.
39224843	Asteraceae genome database: a comprehensive platform for Asteraceae genomics.