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Article has an altmetric score of 73

Grant support

This research was supported by the National Programme for Fostering Excellence in Scientific and Technical Research (Grant No. PGC2018-098073-A-I00 MCIU/AEI/FEDER, UE, to J.H.C.) and the Severo Ochoa Centres of Excellence Programme (Grant No. SEV-2016-0672 (2017-2021) to C.P.C.) from the State Research Agency (AEI) of Spain, as well as a Research Technical Support Staff Aid (PTA2019-017593-I/AEI/10.13039/501100011033 to A.H.P.); European Research Council grant MicroBioS (ERC-2014-AdG)-GA669830 (to P.B.). Cloud computing is supported by BMBF (de.NBI network #031A537B).

Analysis of institutional authors

Cantalapiedra, CpAuthorHernandez-Plaza, AAuthorHuerta-Cepas, JCorresponding Author

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eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Publicated to:Molecular Biology And Evolution. 38 (12): 5825-5829 - 2021-12-01 38(12), DOI: 10.1093/molbev/msab293

Authors: Cantalapiedra, Carlos P.; Hernandez-Plaza, Ana; Letunic, Ivica; Bork, Peer; Huerta-Cepas, Jaime;

Affiliations

Abstract

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: 1) de novo gene prediction from raw contigs, 2) built-in pairwise orthology prediction, 3) fast protein domain discovery, and 4) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnogmapper.embl.de.

Keywords

BioinformaticsComputational genomicsDatabaseDatabases, geneticFunctional annotationGenomicsMetagenomeMetagenomicsMolecular sequence annotationPhylogenySoftware

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Molecular Biology And Evolution due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2021, it was in position 15/175, thus managing to position itself as a Q1 (Primer Cuartil), in the category Genetics & Heredity. Notably, the journal is positioned above the 90th percentile.

This publication has been distinguished as a “Highly Cited Paper” by the agencies WoS (ESI, Clarivate) and ESI (Clarivate), meaning that it ranks within the top 1% of the most cited articles in its thematic field during the year of its publication. In terms of the observed impact of the contribution, this work is considered one of the most influential worldwide, as it is recognized as highly cited. (source consulted: ESI Nov 14, 2024)

And this is evidenced by the extremely high normalized impacts through some of the main indicators of this type, which, although dynamic over time and dependent on the set of average global citations at the time of calculation, already indicate that they are well above the average in different agencies:

  • Normalization of citations relative to the expected citation rate (ESI) by the Clarivate agency: 78.82 (source consulted: ESI Nov 14, 2024)
  • Weighted Average of Normalized Impact by the Scopus agency: 185.86 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 617.16 (source consulted: Dimensions Jun 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-06-08, the following number of citations:

  • WoS: 1522
  • Scopus: 2063
  • OpenCitations: 1719

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-06-08:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 1516.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 1444 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 72.57.
  • The number of mentions on the social network X (formerly Twitter): 56 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Germany; Republic of Korea.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (PEREZ CANTALAPIEDRA, CARLOS) and Last Author (HUERTA CEPAS, JAIME).

the author responsible for correspondence tasks has been HUERTA CEPAS, JAIME.