On the public citation graph
Integration of Structured Biological Data Sources using Biological Expression Language
0 signed · 75 inferred · view as graph
Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.
Is this your work? Sign in with ORCID and put your name on the
claims that are yours.
Reference health. See whether every reference in this work resolves to a
known work and none has been retracted — and get a dated CiteStamped
badge you can embed.
What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/cpbi.5openalex-snapshot
The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses
inferredcites →https://doi.org/10.1016/j.cels.2015.12.004openalex-snapshot
The Molecular Signatures Database Hallmark Gene Set Collection
inferredcites →https://doi.org/10.1016/j.chembiol.2019.02.018openalex-snapshot
Cheminformatics Tools for Analyzing and Designing Optimized Small Molecule Collections and Libraries
inferredcites →https://doi.org/10.1016/j.drudis.2012.05.016openalex-snapshot
Open PHACTS: semantic interoperability for drug discovery
inferredcites →https://doi.org/10.1016/j.drudis.2013.12.011openalex-snapshot
Recent advances in modeling languages for pathway maps and computable biological networks
inferredcites →https://doi.org/10.1016/j.jbi.2008.03.004openalex-snapshot
Bio2RDF: Towards a mashup to build bioinformatics knowledge systems
inferredcites →https://doi.org/10.1017/cbo9781107707221.009openalex-snapshot
Growing the Learning Sciences: Brand or Big Tent? Implications for Graduate Education
inferredcites →https://doi.org/10.1038/msb.2011.77openalex-snapshot
Controlled vocabularies and semantics in systems biology
inferredcites →https://doi.org/10.1038/nbt1210-1308copenalex-snapshot
Erratum: Corrigendum: The BioPAX community standard for pathway data sharing
inferredcites →https://doi.org/10.1038/nmeth.3963openalex-snapshot
Impact of outdated gene annotations on pathway enrichment analysis
inferredcites →https://doi.org/10.1038/nmeth.4077openalex-snapshot
OmniPath: guidelines and gateway for literature-curated signaling pathway resources
inferredcites →https://doi.org/10.1038/npre.2009.3193.1openalex-snapshot
UniProt in RDF: Tackling Data Integration and Distributed Annotation with the Semantic Web
inferredcites →https://doi.org/10.1038/s41540-018-0078-8openalex-snapshot
ComPath: an ecosystem for exploring, analyzing, and curating mappings across pathway databases
inferredcites →https://doi.org/10.1089/cmb.1995.2.557openalex-snapshot
Challenges in Integrating Biological Data Sources
inferredcites →https://doi.org/10.1093/bib/bbv063openalex-snapshot
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases
inferredcites →https://doi.org/10.1093/bib/bby025openalex-snapshot
Navigating the disease landscape: knowledge representations for contextualizing molecular signatures
inferredcites →https://doi.org/10.1093/bib/bby097openalex-snapshot
Comprehensive and critical evaluation of individualized pathway activity measurement tools on pan-cancer data
inferredcites →https://doi.org/10.1093/bioinformatics/btg405openalex-snapshot
affy—analysis of Affymetrix GeneChip data at the probe level
inferredcites →https://doi.org/10.1093/bioinformatics/bth474openalex-snapshot
Microarray data mining with visual programming
inferredcites →https://doi.org/10.1093/bioinformatics/btt547openalex-snapshot
BioServices: a common Python package to access biological Web Services programmatically
inferredcites →https://doi.org/10.1093/bioinformatics/btt765openalex-snapshot
The EBI RDF platform: linked open data for the life sciences
inferredcites →https://doi.org/10.1093/bioinformatics/btw214openalex-snapshot
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases
inferredcites →https://doi.org/10.1093/bioinformatics/btx660openalex-snapshot
PyBEL: a computational framework for Biological Expression Language
inferredcites →https://doi.org/10.1093/bioinformatics/bty719openalex-snapshot
metaGraphite–a new layer of pathway annotation to get metabolite networks
inferredcites →https://doi.org/10.1093/bioinformatics/btz117openalex-snapshot
BioKEEN: a library for learning and evaluating biological knowledge graph embeddings
inferredcites →https://doi.org/10.1093/database/bay103openalex-snapshot
Toward a service-based workflow for automated information extraction from herbarium specimens
inferredcites →https://doi.org/10.1093/database/bay126openalex-snapshot
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language
inferredcites →https://doi.org/10.1093/database/baz068openalex-snapshot
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language
inferredcites →https://doi.org/10.1093/nar/gkq1039openalex-snapshot
Pathway Commons, a web resource for biological pathway data
inferredcites →https://doi.org/10.1093/nar/gkq537openalex-snapshot
The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function
inferredcites →https://doi.org/10.1093/nar/gkr917openalex-snapshot
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
inferredcites →https://doi.org/10.1093/nar/gku1003openalex-snapshot
STRING v10: protein–protein interaction networks, integrated over the tree of life
inferredcites →https://doi.org/10.1093/nar/gku975openalex-snapshot
The complex portal - an encyclopaedia of macromolecular complexes
inferredcites →https://doi.org/10.1093/nar/gkv1048openalex-snapshot
SIGNOR: a database of causal relationships between biological entities
inferredcites →https://doi.org/10.1093/nar/gkw1033openalex-snapshot
Genenames.org: the HGNC and VGNC resources in 2017
inferredcites →https://doi.org/10.1093/nar/gkw1092openalex-snapshot
KEGG: new perspectives on genomes, pathways, diseases and drugs
inferredcites →https://doi.org/10.1093/nar/gkw1102openalex-snapshot
The BioGRID interaction database: 2017 update
inferredcites →https://doi.org/10.1093/nar/gkw1108openalex-snapshot
Expansion of the Gene Ontology knowledgebase and resources
inferredcites →https://doi.org/10.1093/nar/gkw985openalex-snapshot
HIPPIE v2.0: enhancing meaningfulness and reliability of protein–protein interaction networks
inferredcites →https://doi.org/10.1093/nar/gkx1037openalex-snapshot
DrugBank 5.0: a major update to the DrugBank database for 2018
inferredcites →https://doi.org/10.1093/nar/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky1032openalex-snapshot
Human Disease Ontology 2018 update: classification, content and workflow expansion
inferredcites →https://doi.org/10.1109/jproc.2015.2483592openalex-snapshot
A Review of Relational Machine Learning for Knowledge Graphs
inferredcites →https://doi.org/10.1126/science.1257601openalex-snapshot
Uncovering disease-disease relationships through the incomplete interactome
inferredcites →https://doi.org/10.1155/2015/435141openalex-snapshot
Are the Two Human Papillomavirus Vaccines Really Similar? A Systematic Review of Available Evidence: Efficacy of the Two Vaccines against HPV
inferredcites →https://doi.org/10.1155/2015/737168openalex-snapshot
Computational Modelling Approaches on Epigenetic Factors in Neurodegenerative and Autoimmune Diseases and Their Mechanistic Analysis
inferredcites →https://doi.org/10.1186/1471-2105-11-255openalex-snapshot
Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data
inferredcites →https://doi.org/10.1186/1471-2105-7-1openalex-snapshot
Fast-Find: A novel computational approach to analyzing combinatorial motifs
inferredcites →https://doi.org/10.1186/1752-0509-1-58openalex-snapshot
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
inferredcites →https://doi.org/10.1186/s12859-019-2675-yopenalex-snapshot
Prediction of lncRNA-disease associations by integrating diverse heterogeneous information sources with RWR algorithm and positive pointwise mutual information
inferredcites →https://doi.org/10.1186/s12859-019-2863-9openalex-snapshot
PathMe: merging and exploring mechanistic pathway knowledge
inferredcites →https://doi.org/10.1186/s12918-014-0111-5openalex-snapshot
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis
inferredcites →https://doi.org/10.1186/s13059-016-0953-9openalex-snapshot
High-performance web services for querying gene and variant annotation
inferredcites →https://doi.org/10.1371/journal.pone.0131080openalex-snapshot
Biodiversity on the Rocks: Macrofauna Inhabiting Authigenic Carbonate at Costa Rica Methane Seeps
inferredcites →https://doi.org/10.15252/msb.20177651openalex-snapshot
From word models to executable models of signaling networks using automated assembly
inferredcites →https://doi.org/10.25080/majora-92bf1922-00aopenalex-snapshot
Data Structures for Statistical Computing in Python
inferredcites →https://doi.org/10.3233/jad-160222openalex-snapshot
Using Drugs as Molecular Probes: A Computational Chemical Biology Approach in Neurodegenerative Diseases
inferredcites →https://doi.org/10.3233/jad-161148openalex-snapshot
Neuroimaging Feature Terminology: A Controlled Terminology for the Annotation of Brain Imaging Features
inferredcites →https://doi.org/10.4137/bmi.s29511openalex-snapshot
Genomic, Proteomic, and Metabolomic Data Integration Strategies
inferredcites →https://doi.org/10.5555/3026877.3026899openalex-snapshot
TensorFlow: A system for large-scale machine learning
inferredcites →https://doi.org/10.7554/elife.26726openalex-snapshot
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1093/bib/bbaa390openalex-snapshot
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
inferred← citeshttps://doi.org/10.1093/nar/gkaa1024openalex-snapshot
WikiPathways: connecting communities
inferred← citeshttps://doi.org/10.1101/2020.08.12.243766openalex-snapshot
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms
inferred← citeshttps://doi.org/10.1109/tbdata.2021.3050680openalex-snapshot
Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis
inferred← citeshttps://doi.org/10.15252/msb.202211325openalex-snapshot
Automated assembly of molecular mechanisms at scale from text mining and curated databases
inferred← citeshttps://doi.org/10.20944/preprints202007.0123.v1openalex-snapshot
The Status of Causality in Biological Databases for Logical Modeling: Data Resources and Data Retrieval Possibilities
inferred← citeshttps://doi.org/10.3389/fgene.2019.01203openalex-snapshot
The Impact of Pathway Database Choice on Statistical Enrichment Analysis and Predictive Modeling
inferred← citeshttps://doi.org/10.48550/arxiv.2001.10560openalex-snapshot
The KEEN Universe: An Ecosystem for Knowledge Graph Embeddings with a Focus on Reproducibility and Transferability
inferred← citeshttps://doi.org/10.70675/e4ca6537z5926z484fz9de9z8ae5b1e1f63aopenalex-snapshot
Development of new computational methods for a synthetic gene set annotation
Editorial review for independent work. ICSAC — the Institute for Complexity
Science and Advanced Computing — runs a structured editorial panel for researchers
publishing outside journals, and publishes on CiteStamp rails. Submission is free
and goes through ORCID: icsacinstitute.org/submit.