Scientific Research Glossary

An AI system developed by DeepMind that predicts the 3D structure of proteins from their amino acid sequence. Pilus links gene cards to AlphaFold structure predictions via UniProt.

The process of adding biological information to a sequence or structure, such as identifying genes, predicting functions, or marking regulatory elements.

A mechanism of horizontal gene transfer in bacteria, involving the direct transfer of genetic material (typically a plasmid) from a donor cell to a recipient cell through a pilus. This process is a major driver of antibiotic resistance spreading and bacterial evolution.

An interdisciplinary field combining biology, computer science, and statistics to analyze and interpret biological data.

A series of molecular events in a cell leading to a specific outcome. Examples include metabolic pathways, signaling pathways, and gene regulation pathways.

A typed, directional link between two entities that models how scientific knowledge is created and structured. Pilus supports 15 causal relation types including found_in, regulates, authored_by, cites, and studies.

A graph showing relationships between academic papers based on citations. Helps identify influential papers and trace research development.

A registration agency for scholarly publications that provides DOI resolution and metadata lookup. CrossRef allows Pilus to import article metadata from any DOI.

Digital Object Identifier - A persistent identifier used to uniquely identify digital objects, particularly academic publications. Format: 10.xxxx/xxxxx

A graph visualization algorithm that simulates physical forces between nodes to produce aesthetically pleasing layouts. Pilus uses d3-force-3d for both 2D and 3D knowledge graph rendering.

A comprehensive computational model of biological systems providing standardized terms for cellular components, molecular functions, and biological processes.

An abbreviated form of a gene name consisting of italicized letters and sometimes numbers. Official symbols are assigned by HGNC for human genes.

The study of an organism's complete set of DNA, including all genes. Includes both sequencing genomes and analyzing gene function.

Computational analysis of graph structure to extract insights. Pilus includes 8 algorithms: Louvain community detection, bridge nodes, degree centrality, hub nodes, isolated nodes, shortest path, connected components, and global statistics.

HUGO Gene Nomenclature Committee - The authority responsible for approving gene symbols and names for human genes.

A component that automatically analyzes a knowledge graph to suggest new connections. Pilus uses 7 inference rules: transitive paths, same organism, same affiliation, same journal, same year, same location, and co-authorship.

A system that goes beyond simple note-taking by understanding relationships between entities. Pilus is a knowledge engine that connects genes, organisms, articles, researchers, conferences, and processes in a structured graph.

A network of interconnected entities (nodes) and their relationships (edges) used to organize and visualize information. In research, knowledge graphs help scientists connect papers, genes, researchers, and concepts.

A comprehensive survey of scholarly sources on a specific topic, providing an overview of current knowledge and identifying gaps in research.

A community detection algorithm used to identify clusters of densely connected nodes in a graph. In Pilus, it discovers research clusters in your knowledge graph.

A linked series of chemical reactions occurring within a cell, catalyzed by enzymes, that converts a substrate into a product.

A database at the National Center for Biotechnology Information that provides gene-specific information including nomenclature, chromosomal location, gene products, and associated phenotypes.

A curated classification database maintained by the National Center for Biotechnology Information (NCBI) containing ~2.5 million species with their taxonomic lineage, domain, and scientific/common names.

In biology, a structured vocabulary that defines the relationships between biological concepts. Examples: Gene Ontology (GO), Disease Ontology.

Open Researcher and Contributor ID — a persistent digital identifier for researchers that distinguishes them from other contributors. Format: 0000-0000-0000-0000.

From Latin pilus (plural: pili), meaning 'hair'. In microbiology, a pilus is a hair-like appendage found on the surface of bacteria. Pili play a critical role in bacterial conjugation — the process by which bacteria transfer genetic material (DNA) between cells through direct contact. The Pilus app takes its name from this biological structure: just as bacterial pili create bridges between cells to share genetic information, Pilus creates digital bridges between scientific entities (genes, articles, organisms, researchers) to connect and share knowledge across a research network.

PubMed Identifier - A unique numerical identifier assigned to each PubMed record. Used to reference specific scientific articles.

The large-scale study of proteins, particularly their structures and functions. Proteomics is an important component of functional genomics.

A free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. Maintained by the National Library of Medicine (NLM) at the NIH.

A series of molecular events by which a cell converts an extracellular signal into a cellular response through a sequence of biochemical reactions.

The study of the complete set of RNA transcripts produced by the genome under specific conditions. Often measured using RNA-seq or microarrays.

Universal Protein Resource - A comprehensive database of protein sequence and functional information. Combines data from Swiss-Prot, TrEMBL, and PIR-PSD.