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Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database

Florian Malard, Eugenia Wulff-Fuentes, Rex R Berendt, Guillaume Didier, Stephanie Olivier-Van Stichelen
2021 Database: The Journal of Biological Databases and Curation  
We particularly emphasized our workflow, involving a mostly automatized and self-maintained database, including machine learning approaches for text mining.  ...  In this version, more than 14 500 O-GlcNAcylated proteins and 11 000 O-GlcNAcylation sites are referenced from the curation of 2200 publications.  ...  Specifically, we emphasize the smart features of such database, e.g., smart organization, automatization and self-maintenance, while using the O-GlcNAc Database as a case study.  ... 
doi:10.1093/database/baab039 pmid:34279596 pmcid:PMC8288053 fatcat:s5p3bqsr7faj5gcy32exntb5rq

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information

Langho Lee, Kai Wang, Gang Li, Zhi Xie, Yuli Wang, Jiangchun Xu, Shaoxian Sun, David Pocalyko, Jong Bhak, Chulhong Kim, Kee-Ho Lee, Ye Jang (+3 others)
2011 BMC Genomics  
Thus we constructed Liverome, a curated database of liver cancer-related gene signatures with self-contained context information.  ...  Without manual curation, the context information becomes lost, leading to uninformative database contents.  ...  Liverome derives the most informative form of gene signatures through manual curation to construct self-contained database content (right column).  ... 
doi:10.1186/1471-2164-12-s3-s3 pmid:22369201 pmcid:PMC3333186 fatcat:v4yxhdz2ebcp3i4efzlzbeqyre

Unifying data exploration and curation

Shan Shan Huang
2016 Proceedings of the Third International Workshop on Exploratory Search in Databases and the Web - ExploreDB '16  
We discuss the challenges imposed on the database runtime by the use cases of exploration and curation at scale and aspects of the LogicBlox database designed to meet these challenges.  ...  Recent years have seen a surge in "self-service" business intelligence tools.  ...  Shan Shan is published in areas spanning across programming languages, software engineering, and databases.  ... 
doi:10.1145/2948674.2948680 dblp:conf/sigmod/Huang16 fatcat:qd36mpcfbbfhde6osgrx7zoyei

NEPdb: A Database of T-Cell Experimentally-Validated Neoantigens and Pan-Cancer Predicted Neoepitopes for Cancer Immunotherapy

Jiaqi Xia, Peng Bai, Weiliang Fan, Qiming Li, Yongzheng Li, Dehe Wang, Lei Yin, Yu Zhou
2021 Frontiers in Immunology  
Here we present NEPdb, a database that contains more than 17,000 validated human immunogenic neoantigens and ineffective neoepitopes within human leukocyte antigens (HLAs) via curating published literature  ...  With a well-designed search engine and visualization modes, this database would enhance the efficiency of neoantigen-based cancer studies and treatments.  ...  Data Curation and Validation of VND In VND, major efforts were made to ensure the data reliability in our database. All screened papers were further manually read and curated.  ... 
doi:10.3389/fimmu.2021.644637 pmid:33927717 pmcid:PMC8078594 fatcat:6jdfyxu7wnfmpo7l3vqc6pz3se

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura (+9 others)
2011 Nature Precedings  
Collaboration CiAID Text and graphic data are integrated to be self-explanatory for the protein.  ...  CIPRO database is aimed at not only collecting those published data, but also presenting unique information including the unpublished transcriptomic and proteomic data and human curated annotation, for  ...  CIPRO database is aimed at not only collecting those published data, but also presenting unique information including the unpublished transcriptomic and proteomic data and human curated annotation, for  ... 
doi:10.1038/npre.2010.5435 fatcat:w75kd5ai3rc4bhjum5jgho3eku

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments

Toshinori Endo, Keisuke Ueno, Kouki Yonezawa, Katsuhiko Mineta, Kohji Hotta, Yutaka Satou, Lixy Yamada, Michio Ogasawara, Hiroki Takahashi, Ayako Nakajima, Mia Nakachi, Mamoru Nomura (+9 others)
2011 Nature Precedings  
Collaboration CiAID Text and graphic data are integrated to be self-explanatory for the protein.  ...  CIPRO database is aimed at not only collecting those published data, but also presenting unique information including the unpublished transcriptomic and proteomic data and human curated annotation, for  ...  CIPRO database is aimed at not only collecting those published data, but also presenting unique information including the unpublished transcriptomic and proteomic data and human curated annotation, for  ... 
doi:10.1038/npre.2010.5435.1 fatcat:gg7hmt4ldrfkza2srpmvr2hpam

Protein subfamily assignment using the Conserved Domain Database

Jessica H Fong, Aron Marchler-Bauer
2008 BMC Research Notes  
Here, we propose a method for assigning NCBI-curated domains from the Curated Domain Database (CDD) that takes into account the organization of the domains into hierarchies of homologous domain models.  ...  heuristics result in almost 90% of current misclassifications due to missing domain subfamilies being replaced by more generic domain assignments, thereby eliminating a significant amount of error within the database  ...  Acknowledgements Special thanks to Naigong Zhang for database assistance and to Naigong Zhang, Ben Shoemaker, and Carl Kingsford for valuable comments on the manuscript.  ... 
doi:10.1186/1756-0500-1-114 pmid:19014584 pmcid:PMC2632666 fatcat:wvx46fjgpbbqnkafsjozsbrysi

ERMRest: A Collaborative Data Catalog with Fine Grain Access Control

Karl Czajkowski, Carl Kesselman, Robert Schuler
2017 2017 IEEE 13th International Conference on e-Science (e-Science)  
Typically, such metadata are created and maintained in a data catalog by a curator as part of data publication.  ...  Example Policy: Self-Serve Curation This section describes an example policy for facilitating "self-serve data curation" with minimal intervention required by system operators.  ...  We use the term self-serve data curation as the curation of complex data performed directly by domain scientists.  ... 
doi:10.1109/escience.2017.83 pmid:29756002 pmcid:PMC5939964 dblp:conf/eScience/CzajkowskiKS17 fatcat:krdu2qgcinff7ko2k2dhbsbfmu

IPD-MHC 2.0: an improved inter-species database for the study of the major histocompatibility complex

Giuseppe Maccari, James Robinson, Keith Ballingall, Lisbeth A. Guethlein, Unni Grimholt, Jim Kaufman, Chak-Sum Ho, Natasja G. de Groot, Paul Flicek, Ronald E. Bontrop, John A. Hammond, Steven G. E. Marsh
2016 Nucleic Acids Research  
The IPD-MHC Database project (http://www.ebi. ac.uk/ipd/mhc/) collects and expertly curates sequences of the major histocompatibility complex from non-human species and provides the infrastructure and  ...  These sequences are expertly curated and made publicly available through an open access website.  ...  The authors would also like to acknowledge the work of the comparative MHC community in sequencing, identifying and submitting the many sequences, which form the core data that the IPD-MHC Database represents  ... 
doi:10.1093/nar/gkw1050 pmid:27899604 pmcid:PMC5210539 fatcat:n5vvqsbizfeozczarnbskaxwr4

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data

S. Poux, M. Magrane, C. N. Arighi, A. Bridge, C. O'Donovan, K. Laiho
2014 Database: The Journal of Biological Databases and Curation  
Database URL: www.uniprot.org .  ...  By taking the example of sirtuin-5, a complex annotation case, we will describe the curation procedure of UniProtKB/Swiss-Prot and detail how we report conflicting information in the database.  ...  (2) regarding the high number of misannotations in automatically curated databases.  ... 
doi:10.1093/database/bau016 pmid:24622611 pmcid:PMC3950660 fatcat:vbvc34w5cbhe7kbva2rdhwwuzm

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

D. Smedley, P. Schofield, C.-K. Chen, V. Aidinis, C. Ainali, J. Bard, R. Balling, E. Birney, A. Blake, E. Bongcam-Rudloff, A. J. Brookes, G. Cesareni (+18 others)
2010 Database: The Journal of Biological Databases and Curation  
Communities need to acknowledge; (i) a central site where they can find relevant resources would be useful, and; (ii) the only practical means of achieving this is for each database to self-curate its  ...  Although the creators and maintainers of a resource are best placed to describe the associated metadata, a self-curation approach can raise data quality issues, but these should be minimized if the annotation  ... 
doi:10.1093/database/baq014 pmid:20627863 pmcid:PMC2911849 fatcat:cwaam2oayjftbcgepk3uedo5pe

The French National Registry of patients with Facioscapulohumeral muscular dystrophy

Céline Guien, Gaëlle Blandin, Pauline Lahaut, Benoît Sanson, Katia Nehal, Sitraka Rabarimeriarijaona, Rafaëlle Bernard, Nicolas Lévy, Sabrina Sacconi, Christophe Béroud
2018 Orphanet Journal of Rare Diseases  
The questionnaires are sent to the clinical curator who controls the data quality prior to their import into the database.  ...  Clinical and molecular data validation Two levels of data curation are available: the clinical curator can create new patients and new self-reports or clinical evaluation questionnaires, while the molecular  ... 
doi:10.1186/s13023-018-0960-x fatcat:gjame3lodjbkfolbgkuqyif5ci

YARD: A Tool for Curating Research Outputs

Limor Peer, Joshua Dull
2020 Data Science Journal  
This paper describes a curation tool that responds to this challenge by economizing and optimizing curation efforts.  ...  activities of researchers, curators, and publishers through a single pipeline.  ...  Quality and curation in repositories The scientific principle of self-correction asks researchers to be transparent about their design, data, methods, and analysis.  ... 
doi:10.5334/dsj-2020-028 fatcat:vte77t3v7feidhmsneyds3u3mu

A survey of metallo- -lactamase sequence accuracy before the data deluge

K. I. Apagyi, M. J. Ellington
2014 Journal of Antimicrobial Chemotherapy  
Thus errors can, even without automated processes, become self-replicating in a non-curated and 'live' database such as GenBank.  ...  Sequences in such databases are often sourced from GenBank and then subjected to varying amounts of curation.  ... 
doi:10.1093/jac/dku284 pmid:25085656 fatcat:ebsk7i4hmfe77g5ygxcthagq7q

Tracking self-citations in academic publishing

Ameni Kacem, Justin W. Flatt, Philipp Mayr
2020 Scientometrics  
Here, in favor of openly tracking self-citations we report on self-referencing behavior among various academic disciplines as captured by the curated Clarivate Analytics Web of Science database.  ...  Instead we urge academics to embrace visibility of citation data in a community of peers, which relies on nuance and openness rather than curated scorekeeping.  ...  This work was funded by BMBF (Federal Ministry of Education and Research, Germany) under grant number 01PQ17001, the "Analyzing Self-citations in Web of Science (WoS)" project (http://bit.ly/Selfc itati  ... 
doi:10.1007/s11192-020-03413-9 fatcat:ubjiqe3g3bhhrle5r3aor3nkza
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