Evidence map›Paper›PMID 41378136›Full record

ArticleHorticulture research2025

TVIR 2.0: an enhanced database of the vegetables information resources.

Tong Yu, Xiao Ma, Zhuo Liu, Tongbing Su, Chenhao Zhang, Lusheng Guo, Zipeng Meng, Di Guo, Nana Yao, Yingchao Zhang and 2 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Horticulture research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Genome-Wide Characterization of theLife (Basel, Switzerland) · 2026
    Article
  4. Article
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

12 authors.

Tong YuSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.ORCID https://orcid.org/0000-0001-6644-4745
Xiao MaSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Zhuo LiuSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.ORCID https://orcid.org/0000-0002-0172-2166
Tongbing SuState Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China.ORCID https://orcid.org/0000-0002-3411-7341
Chenhao ZhangSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Lusheng GuoSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Zipeng MengSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Di GuoSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Nana YaoSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Yingchao ZhangSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Haibin LiuSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.
Xiaoming SongSchool of Life Sciences/School of Basic Medical Sciences/Library/Key Laboratory for Quality of Salt Alkali Resistant TCM of Hebei Administration of TCM, North China University of Science and Technology, Tangshan 063210, China.ORCID https://orcid.org/0000-0003-0084-3668

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Since its inaugural release in 2022, The Vegetables Information Resources (TVIR) has been a cornerstone for genomics and genetic breeding studies within the vegetable research community. With advancements in sequencing technologies leading to an influx of new genome sequences, TVIR has been upgraded to version 2.0 (http://tvir2.bio2db.com/), expanding from 59 to 84 vegetable species and introducing new functional modules to accelerate research. This upgrade incorporates a CRISPR/Cas9 resource module, which integrates four specialized tools: CasFinder, CasOT, Crisflash, and CRISPRCasFinder, to facilitate gene editing research. The database further features dynamic synteny analysis with an interactive interface, enabling users to visualize genomic relationships between species. Additionally, two novel bioinformatics tools Hmmsearch and CRISPRCasViewer are integrated to enhance comparative and functional genomic analyses. TVIR 2.0 retains all TVIR 1.0 features while updating resistance gene identification, expanding from 3 to 8 types, and transcription factor datasets, now including 237 431 TFs, an increase from 172 493.The database integrates comprehensive genomic, transcriptomic, and functional annotation data, providing freely accessible resources for vegetable breeding and gene editing.

Identifiers

PMID41378136
PMCPMC12685723

What OpenQuestion holds

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Registered trials

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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.