PubMed Labs: an experimental system for improving biomedical literature search

Fiorini, Nicolas; Canese, Kathi; Bryzgunov, Rostyslav; Radetska, Ievgeniia; Gindulytė, Asta; Latterner, Martin; Miller, Vadim; Osipov, Maxim; Kholodov, Michael; Starchenko, Grisha; Kireev, Evgeny; Lu, Zhiyong

doi:10.1093/database/bay094

Cited by 20 publications

(17 citation statements)

References 14 publications

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“…if the myomiR is ever experimentally validated to be a biomarker, the entry in the column will be "Yes" otherwise "No". The reference papers are hyperlinked to PubMed 31 which allows ready access to the original paper. In this format, the expression changes of a myomiR in different durations, tissues, and atrophy-disease conditions can be easily and quickly explored, compared and analysed.…”

Section: Resultsmentioning

confidence: 99%

“…The combination of keywords such "muscle atrophy" and "miRNA"; "muscle wasting" and "miRNA"; "loss of muscle mass" and "miRNA" etc. were used to extract a list 390 publications from PubMed, and Google scholar as in January 2019 31 . After removing redundancy and duplicity, the unique publications were manually curated to identify the Differentially Expressed (DE) miRNAs during muscle-atrophy.…”

Section: Discussionmentioning

confidence: 99%

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MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Gupta

Srivastava

Suryakumar

et al. 2020

Sci Rep

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Muscular atrophy or muscle loss is a multifactorial clinical condition during many critical illnesses like cancer, cardiovascular diseases, diabetes, pulmonary diseases etc. leading to fatigue and weakness and contributes towards a decreased quality of life. The proportion of older adults (>65 y) in the overall population is also growing and aging is another important factor causing muscle loss. Some muscle miRNAs (myomiRs) and their target genes have even been proposed as potential diagnostic, therapeutic and predictive markers for muscular atrophy. MyomirDB (http://www.myomirdb.in/) is a unique resource that provides a comprehensive, curated, user-friendly and detailed compilation of various miRNA bio-molecular interactions; miRNA-Transcription Factor-Target Gene co-regulatory networks and ~8000 tripartite regulons associated with 247 myomiRs which have been experimentally validated to be associated with various muscular atrophy conditions. For each database entry, MyomirDB compiles source organism, muscle atrophic condition, experiment duration, its level of expression, fold change, tissue of expression, experimental validation, disease and drug association, tissue-specific expression level, Gene Ontology and KEGG pathway associations. The web resource is a unique server platform which uses in-house scripts to construct miRNA-Transcription Factor-Target Gene co-regulatory networks and extract tri-partite regulons also called Feed Forward Loops. These unique features helps to offer mechanistic insights in disease pathology. Hence, MyomirDB is a unique platform for researchers working in this area to explore, fetch, compare and analyse atrophy associated miRNAs, their co-regulatory networks and FFL regulons.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Gupta

Srivastava

Suryakumar

et al. 2020

Sci Rep

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show abstract

“…The copyright holder for this this version posted October 4, 2020. ; https://doi.org/10.1101/2020.10.01.20205476 doi: medRxiv preprint 11 artificial intelligence and machine learning developers are aware that searches relying solely on MeSH® index may be out of date and introduce bias. [9] . CC-BY-NC-ND 4.0 International license It is made available under a perpetuity.…”

Section: Discussionmentioning

confidence: 99%

Delay and bias in PubMed medical subject heading (MeSH^®) indexing of respiratory journals

Hadfield

2020

Preprint

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Introduction PubMed is a primary global open-access literature research database. Articles on PubMed are indexed manually with medical subject headings (MeSH) to facilitate more complete literature searches. We aimed to determine the length of delay from publication to MeSH indexing for key respiratory journals and to investigate whether delays are increasing over time and whether there are country or impact-factor specific biases in indexing. Methods PubMed was searched for the keyword asthma for the 10 year period June 2009 to June 2019. MEDLINE fields including journal title, publication date, PubMed entrez date and MeSH indexing date were extracted and delay in indexing was calculated in days. Results Twenty-nine respiratory journals had delay from publication to MeSH indexing ranging from an average of 153.6 days to 409.9 days; 5/29 (17.2%) had never been indexed for PubMed. There was a significantly longer delay in MeSH indexing for UK-based publications (mean delay of 281.7 days) compared to USA-based publications (mean delay of 214.9 days; mean difference 66.8 days, 95% CI 60.8, 72.8, P < 0.0001). Delays in MeSH indexing increased over time. Conclusion There are long and increasing delays in PubMed MeSH indexing of respiratory journals. All PubMed users should be aware that systematic literature searches that rely on MeSH search terms or utilise PubMed filters are likely to exclude recent research and citations from key journals. Researchers and clinicians need to be aware of these delays and biases to ensure their literature searches are both up-to-date and complete.

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“…Among the major global centers, the NCBI (1) reports on new and expanded literature resources, including PubMed Labs (2) a new interface to PubMed, and new sequence database search options. The EBI paper (3) reports on the new databases Single Cell Expression Atlas and PDBe-Knowledgebase.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection

Rigden

Fernández

2018

Nucleic Acids Research

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The 2019 Nucleic Acids Research (NAR) Database Issue contains 168 papers spanning molecular biology. Among them, 64 are new and another 92 are updates describing resources that appeared in the Issue previously. The remaining 12 are updates on databases most recently published elsewhere. This Issue contains two Breakthrough articles, on the Virtual Metabolic Human (VMH) database which links human and gut microbiota metabolism with diet and disease, and Vibrism DB, a database of mouse brain anatomy and gene (co-)expression with sophisticated visualization and session sharing. Major returning nucleic acid databases include RNAcentral, miRBase and LncRNA2Target. Protein sequence databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure. STRING and KEGG update in the section on metabolism and pathways. Microbial genomes are covered by IMG/M and resources for human and model organism genomics include Ensembl, UCSC Genome Browser, GENCODE and Flybase. Genomic variation and disease are well-covered by GWAS Catalog, PopHumanScan, OMIM and COSMIC, CADD being another major newcomer. Major new proteomics resources reporting here include iProX and jPOSTdb. The entire database issue is freely available online on the NAR website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been updated, reviewing 506 entries, adding 66 new resources and eliminating 147 discontinued URLs, bringing the current total to 1613 databases. It is available at http://www.oxfordjournals.org/nar/database/c.

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PubMed Labs: an experimental system for improving biomedical literature search

Cited by 20 publications

References 14 publications

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Delay and bias in PubMed medical subject heading (MeSH^®) indexing of respiratory journals

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection

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PubMed Labs: an experimental system for improving biomedical literature search

Cited by 20 publications

References 14 publications

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

MyomirDB: A unified database and server platform for muscle atrophy myomiRs, coregulatory networks and regulons

Delay and bias in PubMed medical subject heading (MeSH®) indexing of respiratory journals

The 26th annual Nucleic Acids Research database issue and Molecular Biology Database Collection

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Product

Resources

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Delay and bias in PubMed medical subject heading (MeSH^®) indexing of respiratory journals