NAR Database

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NAR Database

5 Why some databases are no longer in the the databases and dropped from it

Authors and curators receive little or no remuneration for their efforts and that it is still difficult to obtain money for creating and maintaining a biological database

Sometimes this is related to the content being available in other databases

Old database or test database is drop after successful migration to a new host

The data is not valid anymore

The data is not update time by time

4 Why we need to group these databases

users can track databases by focusing on specific thing

type and number of databases tha analyse, integrate and summarize the available data keep increasing

easy for up to date

avoid redundancy

ease of search ,collecting , systematizing and sorting into specific category

3 Criteria for selection into NAR databases

rating and evaluation provided

have high level for contribution in research and study

have high impact

rigid originality

open access in HTML and PDF format

provides searching, editing, versioning, history and discussion features

data for each database include a brief description, a URL, a contact email

users can contribute, update and maintain the data in many different ways

Entries can be searched, queried or browsed by category

User’ friendly for novice and experience user

Database are need to be up to date and have recent articles

2 Numbers available

23 obsolete websites has been removed

88 new resources

Total 1685 databases

41 subcategories

15 categories

Articles

17 articles from other journals

95 papers for previous NAR issue

178 -62 papers are for newly created databases

6 Why databases are created and shared

Present as a collection of human-related biological databases and provide a mini-review by classifying them into different categories according to their data types

To provide web application programming interfaces (APIS) for computers to exchange and integrate data from various database resources in an automated manner

To store, organize and share data in a structured and searchable manner with the aim to facilitate data retrieval and visualization for humans

To manage such data deluge is growing at ever-faster rates

To make biological data available in computer-readable form

• Since analysis of biological data almost always involves computers, having the data in computer-readable form rather than printed on paper is a necessary first step

Make biological data available to scientists

• Not all data is actually published explicitly in an article (genome sequences)

• Published data may be difficult to find or access, and collecting it from the literature is very time-consuming.

• as much as possible of a particular type of information should be available in one single place (book, site, database)

7 References

5) http://digitalcuration.blogspot.my/2008/04/thousand-open-molecular-biology.htm

4) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4411498/

3) Dan M. Bolser and etc (2011) MetaBase - the wiki - database of biological databases Nucleic Acids Research, 2012, Vol. 40, Database issue doi:10.1093/nar/gkr1099

2) Rigden, D. J., Fernández-Suárez, X. M., & Galperin, M. Y. (2016). The 2016 database issue of Nucleic Acids Research and an updated molecular biology database collection. Nucleic acids research, 44(D1), D1-D6.

1) https://www.oxfordjournals.org/our_journals/nar/database/c/

8 Prepared by: Group 20

NORAZIERA BINTI AHMAD

AMANINA NADHIRAH BINTI ANUAR

SITI SUHAILA BINTI ZULKEPLE

MOHD HAZIQ IZZUDDIN BIN ROSLI

1 Organisation of databases and its major grouping (as of 2016)

Cell biology

BARD, CloneDB, ExoCarta, DNAtraffic

Immunological databases

ALPSbase, AntigenDB, IEDB, IMGT

Plant databases

AgBase, DOOR, DATF, IC4R

Organelle databases

FUGOID, GOBASE, Organelle DB, PLprot

Other Molecular Biology Databases

BioModels, BioNumbers, SCLD, WormBook

Proteomics Resources

BIOZON,CPLM,dbSNO,MOPED

Microarray Data and other Gene Expression Databases

CEBS, CAGE, EMAGE, GEISHA

Human Genes and Diseases

DIDA, GeneWiki, NECTAR, TSGene

Human and other Vertebrate Genomes

AgBase, ENCODE DCC, FANTOM, GeneAnnot

Metabolic and Signaling Pathways

KEGG, MetaCyc, Reactome, WikiPathways

Genomics Databases (non-vertebrate)

BioGPS, GO, superCAT, IDBD

Structure Databases

BARD, DrugBank, CheBI, mVOC

Protein sequence databases

Pfam, PANTHER, eggNOG, GPCRdb, TCDB, MEROPS

RNA sequence databases

dbRES, ARED, BPS, miREX

Nucleotide Sequence Databases

CEGA, JuncDB ,dbSUPER , SEA ,Dfam