Identity
Canonical name: KEScience PaperBLAST. 1
Known alias: PaperBLAST. 1
Stable external identifier: No stable external identifier is reported in the source document. 1
KEScience PaperBLAST is a dataset containing curated gene assignments derived from literature. 1 The PaperBLAST explorer supports and broadens this description: the kescience_paperblast collection contains 12.4 million rows across 14 tables linking protein sequences and genes to literature, curated annotations, structural data, and PubMed Central full-text snippets. 2
The Caulobacter analysis refines this description by showing that PaperBLAST retrieval can miss known genes under naming-convention differences: its screen returned 0 hits for LpxA, LpxC, LpxD, and LpxK, and 1 for LpxB, versus 11, 15, 15, 18, and 18 NCBI hits, respectively. 3 The report characterized this as an approximately 80% false-negative rate for the tested Caulobacter lipid A genes, while retaining cross-species absence conclusions only when independently supported by NCBI annotation and literature. 3
Key Facts
The BERDL Data Atlas inventory contains 255,096 PaperBLAST curated gene assignments. 1 The explorer supports this inventory figure by listing curatedgene with 255,096 curated annotations. 2
The atlas lists kescience_paperblast among the literature resources recommended for data-use planning, alongside kescience pubmed. 1
PaperBLAST is part of the broader KBase Data Lakehouse inventory of 1,740 deduplicated tables across 119 databases, 17 tenants, and 10 funding agencies or programs. 1
The explorer refines expectations about coverage: 551K (65.6%) of 841K genes with any text-mined paper link have exactly one paper, and at 50% sequence identity, 31,653 protein families have zero papers while 159,046 have exactly one. 2 It also identifies 5,218 multi-member families representing 14,534 sequences with no literature. 2
A cross-database analysis found 129,823 VIMSS cross-references linking PaperBLAST to the Fitness Browser, providing a literature-to-fitness bridge. 2
The Caulobacter result supports using PaperBLAST as a literature-oriented scouting resource but refines its interpretation: naming-convention false negatives mean that absence of a PaperBLAST hit should not by itself establish absence of a gene or pathway. 3
Related Pages
- BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies — source summary describing the PaperBLAST inventory and recommended uses.
- PaperBLAST Data Explorer — Literature Coverage Bias in Protein Sequence Space — source summary quantifying PaperBLAST’s literature concentration, protein-family coverage, and Fitness Browser linkage.
- Regulatory and proteomic architecture of Δfur-permitted lipid A loss in *Caulobacter crescentus* — source summary documenting PaperBLAST retrieval limits in Caulobacter lipid A-gene comparisons.
- kescience pubmed — related KEScience literature dataset.
- uniprot — reference protein resource listed alongside PaperBLAST in the atlas.