WormBase release WS248

The newly released WS248 version of WormBase includes several updates based on curation topics as well as synchronisation with other databases.
In addition the use of Gene Ontology has been extended.

microRNA update for Brugia malayi

The newest data on Brugia malayi microRNAs from miRBase Release 21 has been integrated,
which includes pre-miRNA and mature transcripts as well as the consolidation of
nomenclature used by WormBase and miRBase.

Heavy Metal Topic curation

This release focuses on the curation of data related to Heavy Metal response in nematodes.
Supporting data and publications have been added to WormBase, in addition to review of
gene models for genes involved in this pathway.

New automated descriptions

Gene descriptions generated automatically using a new in-house pipeline were rolled out
for C. elegans in the WS247 release. This release extends that to all other core
species (B. malayi, O. volvulus, C. briggsae, C. brenneri, C. remanei, C. japonica)

New Gene Ontology Annotation Class

Starting with the WS248 release, Gene Ontology annotations will be represented in a new class,
GO_annotation. The GO_annotation class modelsGO annotations as distinct objects in the
database and allows for richer representation of GO data. For example, the GO_annotation
class contains information on interacting genes for annotations that use the IGI (Inferred
from Genetic Interaction) and IPI (Inferred from Physical Interaction) evidence codes, and
also contains annotation extensions that provide additional context for GO terms, such as
substrates for enzymatic activities. The GO_annotation class also includes annotations from
external groups such as UniProt and the Gene Ontology Consortium’s phylogenetic annotation
efforts using PAINT.

WS248: Parasite Papers II

For the upcoming WS248 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Doharey PK, Suthar MK, Verma A, Kumar V, Yadav S, Balaramnavar VM, Rathaur S, Saxena AK, Siddiqi MI, Saxena JK. Molecular cloning and characterization of Brugia malayi thymidylate kinase. Acta Trop. 2014 May;133:83-92. doi:10.1016/j.actatropica.2014.02.003. Epub 2014 Feb 17.

genes referred to: Bm5401

Singh VK, Doharey PK, Kumar V, Saxena JK, Siddiqi MI, Rathaur S, Narender T.
Synthesis, molecular docking and Brugia malayi thymidylate kinase (BmTMK) enzyme inhibition study of novel derivatives of [6]-shogaol. Eur J Med Chem. 2015 Mar 26;93:74-82. doi: 10.1016/j.ejmech.2015.01.035. Epub 2015 Jan 20.

genes referred to: Bm5401

Bulman CA, Bidlow CM, Lustigman S, Cho-Ngwa F, Williams D, Rascón AA Jr, Tricoche N, Samje M, Bell A, Suzuki B, Lim KC, Supakorndej N, Supakorndej P, Wolfe AR, Knudsen GM, Chen S, Wilson C, Ang KH, Arkin M, Gut J, Franklin C,
Marcellino C, McKerrow JH, Debnath A, Sakanari JA. Repurposing auranofin as a lead candidate for treatment of lymphatic filariasis and onchocerciasis. PLoS Negl Trop Dis. 2015 Feb 20;9(2):e0003534. doi: 10.1371/journal.pntd.0003534. eCollection 2015 Feb.

genes referred to: Bma-trxr-1

WS248: Parasite Papers I

For the upcoming WS248 release, a set of new papers have been added to the WormBase database. Some papers of interest to the parasite community are shown below.

Singh AR, Joshi S, Arya R, Kayastha AM, Srivastava KK, Tripathi LM, Saxena JK. Molecular cloning and characterization of Brugia malayi hexokinase. Parasitol Int. 2008 Sep;57(3):354-61. doi: 10.1016/j.parint.2008.03.004. Epub 2008 Apr 9.

genes referred to: Bm4678

Poole CB, Davis PJ, Jin J, McReynolds LA. Cloning and bioinformatic identification of small RNAs in the filarial nematode, Brugia malayi. Mol Biochem Parasitol. 2010 Feb;169(2):87-94. doi: 10.1016/j.molbiopara.2009.10.004. Epub 2009 Oct 27.

linked miRNA genes can be found at the WBPaper00046326 page

Singh N, Heneberg P, Singh N, Singh SK, Rathaur S. Identification of a novel stress regulated FERM domain containing cytosolic protein having PTP activity in Setaria cervi, a bovine filarial parasite. Biochem Biophys Res Commun. 2015 Feb 27;458(1):194-200. doi: 10.1016/j.bbrc.2015.01.100. Epub 2015 Jan 31.

genes referred to: Bma-ptp-1 , ptp-1

Devarajan E, Mishra PK, Thirugnanam S, Mehta K, Chandrashekar R, Perumal K. Molecular characterization of a Brugia malayi transglutaminase. Parasitol Res. 2004 Jun;93(2):145-50. Epub 2004 May 1.

genes referred to: Bma-pdi-3