ArticleBioinformatics advances2025
EMICSS: added-value annotations for EMDB entries.
Article in Bioinformatics advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 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
2 citing papers in PubMed.
- Chart builder: an interactive tool for user driven data visualization in the electron microscopy data bank.Frontiers in bioinformatics · 2026Article
- CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology.GigaScience · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The electron microscopy data bank (EMDB) is a key repository for three-dimensional electron microscopy (3DEM) data but lacks comprehensive annotations and connections to many related biological, functional, and structural data resources. This limitation arises from the optional nature of such information to reduce depositor burden and the complexity of maintaining up-to-date external references, often requiring depositor consent. To address these challenges, we developed EMDB Integration with Complexes, Structures, and Sequences (EMICSS), an independent system that automatically updates cross-references with over 20 external resources, including UniProt, AlphaFold DB, PubMed, Complex Portal, and Gene Ontology. Results: EMICSS (https://www.ebi.ac.uk/emdb/emicss) annotations are accessible in multiple formats for every EMDB entry and its linked resources, and programmatically via the EMDB application programming interface. EMICSS plays a crucial role supporting the EMDB website, with annotations being used on entry pages, statistics, and in the search system. Availability and implementation: EMICSS is implemented in Python and it is an open-source, distributed under the Apache license version 2.0, with core code available on GitHub (https://github.com/emdb-empiar/added_annotations).
Identifiers
What Socratic 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 Socratic graph.