Evidence map›Paper›PMID 41003686›Full record

ArticleJournal of molecular evolution2025

OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.

Ali Yazdizadeh Kharrazi, Adrian M Altenhoff, Nikolai Romashchenko, Christophe Dessimoz, Sina Majidian

Abstract read
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In one paragraph

Article in Journal of molecular evolution, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Review
  2. Perspectives on Orthology During the Quest for Orthologs.Journal of molecular evolution · 2025
    Article
  3. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Ali Yazdizadeh KharraziDataChef, The Hague, The Netherlands.ORCID 0000-0002-2226-4125
Adrian M AltenhoffComputer Science, ETH Zurich, Universitätstr. 6, 8092, Zurich, Switzerland.ORCID 0000-0001-7492-1273
Nikolai RomashchenkoSIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.ORCID 0000-0002-2264-5219
Christophe DessimozSIB Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.ORCID 0000-0002-2170-853X
Sina MajidianDepartment of Computer Science, Johns Hopkins University, 3400 North Charles St., Baltimore, MD, 21218, USA. smajidi5@jhu.edu.ORCID 0000-0001-5345-6982

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The OrthoXML file is a standard file format for orthology data. It provides a standardized structure for describing orthologous and paralogous relationships while allowing the user to store custom and database-specific data in the same format. Although many orthology databases use it as a way to export data, there is no comprehensive toolkit for working with this format. Here, we introduce the OrthoXML-tools ( https://github.com/DessimozLab/orthoxml-tools ), a comprehensive toolkit for loading, manipulating, and exporting the OrthoXML files to other formats. We show its capabilities and performance on our benchmarks.

Indexed as

Computational BiologySoftwareDatabases, GeneticComparative genomicsHierarchical orthologous groupsOrthologyOrthoXML

Identifiers

PMID41003686

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.