The 2013 NAR Database Issue and the online Molecular Biology Database Collection

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The 2013 NAR Database Issue and the online Molecular Biology Database Collection by Mind Map: The 2013 NAR Database Issue and the online Molecular Biology Database Collection

1. (F) Conclusion

1.1. The structural databases featured in this issue show a trend towards

1.1.1. a better integration and cross-referencing tools.

1.1.2. a better understanding of genomic data.

1.1.3. a better treatment of human disease.

2. (E) Curation of the NAR Database Collection

2.1. Clean-up of the collection

2.1.1. One of the authors (XMFS) devised and set in motion a semi-automated procedure

2.1.1.1. To identify obsolete and non-responsive websites

2.1.1.1.1. >90% of the databases listed in the last year’s release of the online Collection were found to be functional

2.1.1.1.2. Close to a hundred of authors who own non-responsive resources had been contacted

2.1.1.1.3. 44 websites (~3.2% of the total) have been approved for deletion

2.1.1.1.4. About 100 entries in the Collection have been updated by

2.2. Reasons of some databases are no longer found in the databases and dropped from it

2.2.1. Some of the resources have been integrated into larger projects

2.2.2. The annotation of human genome has improved and this cause the decreases in the number of resources which cover specific area of genome

2.2.3. Some databases take the commercial route and does not provide a free version articles

2.3. Reasons of creating databases

2.3.1. Promote consistent data entry and retrieval

2.3.2. Reduce the existence of duplicate data among the database tables

2.3.3. Ensure that the up-to-date and accurate information data is available when users need it

2.4. Reasons of sharing databases

2.4.1. Enable users to limit the number of network connections required between the local server and the remote server

2.4.2. Lead to more network connections in single-user scenarios

2.5. Reasons of grouping databases

2.5.1. Allow to summarize data from existing database records

2.5.2. Easy to select the data from massive sources

3. (D) Human Disease Genomics

3.1. Databases cover:

3.1.1. Human genome

3.1.1.1. Ensembl and ENCODE projects

3.1.1.2. UCSC Genome Browser

3.1.1.3. Japanese H-InvDB database

3.1.2. Genomes of model organisms

3.1.2.1. FlyBase

3.1.2.2. Mouse Genome database

3.1.2.3. Xenbase

3.1.2.4. ZFIN

3.1.2.5. Two new databases

3.1.2.5.1. RhesusBase and NHPRTR

3.2. Impact of the genomic data

3.2.1. Fighting for cancer disease

3.2.1.1. Obtained updates from:

3.2.1.1.1. UCSC Cancer Genome Browser

3.2.1.1.2. Atlas of Genetics and Cytogenetics in Oncology and Haematology

3.2.1.1.3. TP53 website

3.2.1.2. Studying cancer at the level of specific cell lines

3.2.1.2.1. CellLineNavigator database

3.2.1.2.2. Genomics of Drug Sensitivity in Cancer (GDSC)

4. (C) New and Updated Databases

4.1. Two databases of DNA repeat elements

4.1.1. Contribute to a better understanding of eukaryotic repeat elements

4.1.1.1. Dfam

4.1.1.2. SINEBase

4.2. Transcriptional factors and transcriptional factor-binding sites

4.2.1. Cover transcriptional factors:

4.2.1.1. TFClass

4.2.1.1.1. Offers a classification of human TFs

4.2.1.2. NPIDB

4.2.1.2.1. Presents structural information on DNA–protein and RNA–protein complexes

4.2.2. Cover TF-binding sites:

4.2.2.1. Factorbook

4.2.2.1.1. TF-binding data from the ENCODE project

4.2.2.2. HOCOMOCO

4.2.2.2.1. Collection of human TF-binding sites

4.2.2.3. CTCFBSDB

4.2.2.3.1. CCCTC-binding factor (CTCF)-binding sites

4.2.2.4. RegulonDB

4.2.2.4.1. Transcriptional regulation in E. coli

4.2.2.5. SwissRegulon

4.2.2.5.1. Regulatory sites in human, mouse and yeast genomes and in model bacteria

4.3. Aspects of protein structure and protein–protein interactions

4.3.1. RCSB Protein Data Bank (PDB)

4.3.2. CATH

4.3.3. PDBTM

4.3.4. EBI's SIFTS

4.3.4.1. Joint effort of UniProt and PDBe

4.3.4.1.1. To provide a residue level mapping of their entries and supplement it with annotation from other public databases

4.3.5. Genome3D

4.3.5.1. A recent collaborative project

4.3.5.1.1. To provide structural annotation from CATH and SCOP to the genomic sequences

4.3.6. dcGO

4.3.6.1. Develops domain-centric ontologies to link protein domains with functions, phenotypes and diseases

4.4. Metagenomic and rRNA sequence analysis

4.4.1. SILVA

4.4.1.1. Widely used comprehensive database of bacterial, archaeal and eukaryotic 16S/18S and 23S/28S rRNA sequences

4.4.2. Description of Protist Ribosomal Reference database (PR2)

4.4.2.1. New database that catalogs small subunit rRNA sequences from unicellular eukaryotes

4.4.3. Ribosomal Database Project

4.4.3.1. Constant feature of the NAR Database Issue since 1991, was last published in 2009

4.4.4. Rfam

4.4.4.1. The universally acclaimed database of RNA families, as well as several databases on long non-coding RNA, microRNA and their targets

4.4.5. MODOMICS

4.4.5.1. RNA modification that is now supplemented by RNApathwaysDB

4.5. Four databases specifically dedicated to Escherichia coli

4.5.1. Update articles on

4.5.1.1. EcoGene

4.5.1.2. EcoCyc

4.5.1.3. RegulonDB

4.5.2. Description of the newly developed E.coli Metabolome Database

4.6. Criteria for selection into NAR database

4.6.1. 1. Quality of atomic co-ordinate data

4.6.2. 2. Sequence unique

4.6.3. 3. Conformation unique

5. (B) History of NAR Database Issue

5.1. Offered descriptions of nucleotide sequence databases

5.1.1. Published in

5.1.1.1. April of 1991

5.1.1.1.1. consisted of 18 articles

5.1.1.2. May of 1992

5.1.1.2.1. consisted of 19 articles

5.1.1.3. July of 1993

5.1.1.3.1. consisted of 24 articles

5.1.1.4. September of 1994

5.1.1.5. January of 1996

5.1.1.6. January of every year

5.2. Examples of articles remained largely the same as 20 years ago:

5.2.1. International Nucleotide Sequence Database collaboration, INSDC

5.2.1.1. collaborated by

5.2.1.1.1. GenBank

5.2.1.1.2. European Nucleotide Archive

5.2.1.1.3. DNA Data Bank of Japan

5.2.2. SWISS-PROT and PIR (now combined into UniProt)

5.2.3. PROSITE

6. (A) Introduction

6.1. 1512 databases

6.1.1. 15 categories and 41 subcategories

6.1.1.1. Nucleotide Sequence Databases

6.1.1.2. RNA sequence databases

6.1.1.3. Protein sequence databases

6.1.1.4. Structure Databases

6.1.1.5. Genomics Databases (non-vertebrate)

6.1.1.6. Metabolic and Signaling Pathways

6.1.1.7. Human and other Vertebrate Genomes

6.1.1.8. Human Genes and Diseases

6.1.1.9. Microarray Data and other Gene Expression Database

6.1.1.10. Proteomics Resources

6.1.1.11. Other Molecular Biology Database

6.1.1.12. Organelle databases

6.1.1.13. Plant databases

6.1.1.14. Immunological databases

6.1.1.15. Cell biology

6.1.2. 176 articles

6.1.2.1. 88 articles describe new online molecular biology databases

6.1.2.1.1. 77 update articles on databases that have been previously featured in the NAR Database Issue

6.1.2.1.2. 11 articles with updates on database resources whose descriptions have been previously published in other journals

6.1.2.2. Another 88 articles provide updates on the databases previously featured in NAR and other journals

6.1.3. Freely available online

7. Group 12 members (3SQB)

7.1. LAU HUI MIN

7.1.1. AQ 100049

7.2. LEE LI SIN

7.2.1. AQ 100051

7.3. SOH WEI CHI

7.3.1. AQ 100078

7.4. TUE SIANG WEI

7.4.1. AQ 100084