ReviewMicrobial biotechnology2018
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects.
Review in Microbial biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Differences in GenBank and RefSeq annotations may affect genomics data interpretation formSphere · 2025Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.Genome research · 2025Article
- Artificial intelligence-based prediction of pathogen emergence and evolution in the world of synthetic biology.Microbial biotechnology · 2024Review
- Multi-omics analysis reveals genes and metabolites involved in Streptococcus suis biofilm formation.BMC microbiology · 2024Article
- Combining DNA and protein alignments to improve genome annotation with LiftOn.bioRxiv : the preprint server for biology · 2024Article
- DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments.Biology · 2024Article
- Exposing the small protein load of bacterial life.FEMS microbiology reviews · 2023Review
- A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.Microbial biotechnology · 2023Review
- An informatic workflow for the enhanced annotation of excretory/secretory proteins ofComputational and structural biotechnology journal · 2023Article
- Protection of the human gene research literature from contract cheating organizations known as research paper mills.Nucleic acids research · 2022Review
- Propagation, detection and correction of errors using the sequence database network.Briefings in bioinformatics · 2022Review
- Article
- Decoding microbial genomes to understand their functional roles in human complex diseases.iMeta · 2022Review
- Identification of human gene research articles with wrongly identified nucleotide sequences.Life science alliance · 2022Article
- In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.Microbial biotechnology · 2022Article
- AnnotaPipeline: An integrated tool to annotate eukaryotic proteins using multi-omics data.Frontiers in genetics · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.PLoS computational biology · 2021Article
- Will Plant Genome Editing Play a Decisive Role in "Quantum-Leap" Improvements in Crop Yield to Feed an Increasing Global Human Population?Plants (Basel, Switzerland) · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Science and engineering rely on the accumulation and dissemination of knowledge to make discoveries and create new designs. Discovery-driven genome research rests on knowledge passed on via gene annotations. In response to the deluge of sequencing big data, standard annotation practice employs automated procedures that rely on majority rules. We argue this hinders progress through the generation and propagation of errors, leading investigators into blind alleys. More subtly, this inductive process discourages the discovery of novelty, which remains essential in biological research and reflects the nature of biology itself. Annotation systems, rather than being repositories of facts, should be tools that support multiple modes of inference. By combining deduction, induction and abduction, investigators can generate hypotheses when accurate knowledge is extracted from model databases. A key stance is to depart from 'the sequence tells the structure tells the function' fallacy, placing function first. We illustrate our approach with examples of critical or unexpected pathways, using MicroScope to demonstrate how tools can be implemented following the principles we advocate. We end with a challenge to the reader.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.