View in EDS

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

Saved in:
Bibliographic Details
Title: OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.
Authors: Yazdizadeh Kharrazi, Ali1 (AUTHOR), Altenhoff, Adrian M.2,3 (AUTHOR), Romashchenko, Nikolai3,4 (AUTHOR), Dessimoz, Christophe3,4 (AUTHOR), Majidian, Sina5 (AUTHOR) smajidi5@jhu.edu
Source: Journal of Molecular Evolution. Dec2025, Vol. 93 Issue 6, p800-805. 6p.
Subjects: Standardization, Utilities (Computer programs), Databases, Comparative genomics, Metadata, Computer file management, Data release
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. [ABSTRACT FROM AUTHOR]
Copyright of Journal of Molecular Evolution is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
FullText Text:
  Availability: 0
Header DbId: egs
DbLabel: Engineering Source
An: 190589415
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Yazdizadeh+Kharrazi%2C+Ali%22">Yazdizadeh Kharrazi, Ali</searchLink><relatesTo>1</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Altenhoff%2C+Adrian+M%2E%22">Altenhoff, Adrian M.</searchLink><relatesTo>2,3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Romashchenko%2C+Nikolai%22">Romashchenko, Nikolai</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Dessimoz%2C+Christophe%22">Dessimoz, Christophe</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Majidian%2C+Sina%22">Majidian, Sina</searchLink><relatesTo>5</relatesTo> (AUTHOR)<i> smajidi5@jhu.edu</i>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22Journal+of+Molecular+Evolution%22">Journal of Molecular Evolution</searchLink>. Dec2025, Vol. 93 Issue 6, p800-805. 6p.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Standardization%22">Standardization</searchLink><br /><searchLink fieldCode="DE" term="%22Utilities+%28Computer+programs%29%22">Utilities (Computer programs)</searchLink><br /><searchLink fieldCode="DE" term="%22Databases%22">Databases</searchLink><br /><searchLink fieldCode="DE" term="%22Comparative+genomics%22">Comparative genomics</searchLink><br /><searchLink fieldCode="DE" term="%22Metadata%22">Metadata</searchLink><br /><searchLink fieldCode="DE" term="%22Computer+file+management%22">Computer file management</searchLink><br /><searchLink fieldCode="DE" term="%22Data+release%22">Data release</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: 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. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Journal of Molecular Evolution is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=egs&AN=190589415
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1007/s00239-025-10271-7
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 6
        StartPage: 800
    Subjects:
      – SubjectFull: Standardization
        Type: general
      – SubjectFull: Utilities (Computer programs)
        Type: general
      – SubjectFull: Databases
        Type: general
      – SubjectFull: Comparative genomics
        Type: general
      – SubjectFull: Metadata
        Type: general
      – SubjectFull: Computer file management
        Type: general
      – SubjectFull: Data release
        Type: general
    Titles:
      – TitleFull: OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Yazdizadeh Kharrazi, Ali
      – PersonEntity:
          Name:
            NameFull: Altenhoff, Adrian M.
      – PersonEntity:
          Name:
            NameFull: Romashchenko, Nikolai
      – PersonEntity:
          Name:
            NameFull: Dessimoz, Christophe
      – PersonEntity:
          Name:
            NameFull: Majidian, Sina
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 01
              M: 12
              Text: Dec2025
              Type: published
              Y: 2025
          Identifiers:
            – Type: issn-print
              Value: 00222844
          Numbering:
            – Type: volume
              Value: 93
            – Type: issue
              Value: 6
          Titles:
            – TitleFull: Journal of Molecular Evolution
              Type: main
ResultId 1