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- | Species **[[Other nematodes|Other nematodes]]5 KB (641 words) - 08:30, 27 September 2010
- ?Species Common_name ?Text Protein ?Protein XREF Species411 bytes (44 words) - 09:14, 17 August 2010
- ''Caenorhabditis species 9'' is a gonochoristic species in Clade V<br> ...ation by C. species 7. Since species 9 has mostly species 9 genes and some species 7 genes, there is actually added value to having it, as long as people know627 bytes (83 words) - 10:05, 3 February 2012
- ''Caenorhabditis sp. 5'' is a member of the Elegans group of species, gonochoristic species, requiring mating between males and females for2 KB (301 words) - 09:54, 28 March 2017
- ''Caenorhabditis species 11'' is a androdioecious species in Clade V<br> [[Category:Other species]]286 bytes (30 words) - 15:58, 15 December 2011
- ''Caenorhabditis species 7'' is a gonochoristic species in Clade V<br> [[Category:Other species]]283 bytes (30 words) - 16:01, 15 December 2011
- ===Nematode Species Mentioned in Titles and Abstracts of Current Papers===525 bytes (60 words) - 15:34, 17 May 2016
- Whenever a new species is added, we need to update the website in several places. ...cedure described below is for non-core species (aka Tier III). When a core-species (aka Tier II) is added, which shouldn't happen too often, different steps n802 bytes (113 words) - 14:10, 10 April 2014
- *Survey organism databases for methods of presenting and navigating between species. *Codify best practices for presentation of multiple species data.885 bytes (118 words) - 16:42, 9 November 2010
- 36 bytes (3 words) - 09:22, 5 January 2011
- ...dentify strengths and weaknesses, we'll first start with a quick survey of other MODs. This will further a second goal of creating a current list of availa430 bytes (67 words) - 16:41, 9 November 2010
- #REDIRECT [[Working Group:Handling Multiple Species:2010.11.09]]64 bytes (6 words) - 16:41, 9 November 2010
Page text matches
- ''Caenorhabditis species 9'' is a gonochoristic species in Clade V<br> ...ation by C. species 7. Since species 9 has mostly species 9 genes and some species 7 genes, there is actually added value to having it, as long as people know627 bytes (83 words) - 10:05, 3 February 2012
- ...ies Class, the removal of an XREF from the ?Species class and addition of ?Species to a small number of classes. > // Species class1 KB (124 words) - 11:01, 19 April 2011
- ''Caenorhabditis species 11'' is a androdioecious species in Clade V<br> [[Category:Other species]]286 bytes (30 words) - 15:58, 15 December 2011
- ''Caenorhabditis species 7'' is a gonochoristic species in Clade V<br> [[Category:Other species]]283 bytes (30 words) - 16:01, 15 December 2011
- ...a genome browser for species-x, type in a C. elegans gene name and get the species-x ortholog(s).189 bytes (30 words) - 17:58, 16 August 2010
- == Species page == ...from WB ParaSite release 16 - how can we update this webpage with the new species? Update from last week864 bytes (136 words) - 15:41, 21 October 2021
- ''Caenorhabditis elegans'' is the best-characterized species in the ''Caenorhabditis'' genus, or, for that matter, in the nematode phylu ...w.wormbook.org/chapters/www_quicktourdiversity/quicktourdiversity.html all other nematodes] is described in WormBook, as is what little is known of its [htt2 KB (214 words) - 15:45, 15 December 2011
- ...s that may suggest assembly errors. It is intended mainly for the species other than ''C. elegans'' as these errors are more likely to be corrected.317 bytes (48 words) - 18:21, 16 August 2010
- Whenever a new species is added, we need to update the website in several places. ...cedure described below is for non-core species (aka Tier III). When a core-species (aka Tier II) is added, which shouldn't happen too often, different steps n802 bytes (113 words) - 14:10, 10 April 2014
- ''Bursaphelenchus xylophilus'' is a gonochoristic species in Clade IV<br> [[Category:Other species]]264 bytes (27 words) - 13:49, 27 March 2012
- ''Caenorhabditis drosophilae'' is a species in Clade V<br> [[Category:Other species]]247 bytes (25 words) - 16:17, 15 December 2011
- ''Ascaris suum'' is a gonochoristic species in Clade III<br> [[Category:Other species]]256 bytes (27 words) - 16:14, 15 December 2011
- ''Steinernema carpocapsae'' is a gonochoristic species in Clade V<br> [[Category:Other species]]282 bytes (29 words) - 16:09, 15 December 2011
- ''Trichinella spiralis'' is a gonochoristic species in Clade I<br> [[Category:Other species]]279 bytes (29 words) - 16:16, 15 December 2011
- ||/Transcript/Origin[1]/Species[1]/Species[1]368 bytes (41 words) - 20:17, 2 May 2013
- Species ?Species300 bytes (27 words) - 08:59, 5 October 2010
- ||/CDS/Origin[1]/Species[1]/Species[1]447 bytes (50 words) - 20:12, 2 May 2013
- = Browse Species = * '''#species''': show the Genus list.1 KB (193 words) - 15:28, 19 June 2014
- == New Species for WS241 == === New Core Species ===2 KB (309 words) - 19:45, 5 December 2013
- ||/Protein/Origin[1]/Species[1]/Species[1]476 bytes (56 words) - 20:17, 2 May 2013
- ?Species Common_name ?Text Protein ?Protein XREF Species411 bytes (44 words) - 09:14, 17 August 2010
- ===Nematode Species Mentioned in Titles and Abstracts of Current Papers===525 bytes (60 words) - 15:34, 17 May 2016
- *Survey organism databases for methods of presenting and navigating between species. *Codify best practices for presentation of multiple species data.885 bytes (118 words) - 16:42, 9 November 2010
- === Support for 'non-canonical' species at the Alliance === ...ical issues surrounding support for 'non-canonical' species (those species other than the main 8 currently supported at the Alliance)2 KB (348 words) - 17:52, 2 February 2023
- ===Handling species lists=== * Handling species in WormBase and Alliance3 KB (440 words) - 08:42, 3 September 2020
- ||/Gene/Identity/Species/Species962 bytes (119 words) - 20:15, 2 May 2013
- ...nding page -e.g. under species menu. Show both assemblies. Advertise other species genomes on blog/news. * Discussion on giving WormBase IDs for other species. Michael P: for people tend to use genebank IDs is not obvious to map/searc929 bytes (147 words) - 19:14, 21 February 2013
- ...ember of the Elegans group, but the Elegans group's closest known outgroup species. It was selected for genomic sequencing on account of its providing the bes 1. A [http://dx.doi.org/10.1163/156854102321122557 species description article] in [http://www.ingentaconnect.com/content/brill/nemy '2 KB (264 words) - 16:01, 15 December 2011
- Origin Species UNIQUE ?Species930 bytes (84 words) - 14:02, 4 October 2010
- ...o species objects as the taxon I'd in the file is different to that in the species object in WormBase.704 bytes (104 words) - 12:27, 28 January 2014
- = Species Collection = It represents the species list as returned by the API.998 bytes (168 words) - 15:29, 19 June 2014
- == 3. Cross species searching; debug GBrowse search (Norie; 10 minutes) == http://dev.wormbase.org:9004/species/gene/WBGene00006763681 bytes (71 words) - 21:26, 12 January 2011
- ''Caenorhabditis brenneri'' is a gonochoristic (male-female) species closely related to ''C. elegans'' (i.e., a fellow member of the Elegans gro ...t has had several formal or informal synonyms, such as "''Caenorhabditis'' species 4" ("''C''. sp. 4"), "''C''. sp. CB5161" (or just "CB5161"), and "''C''. sp2 KB (291 words) - 15:59, 15 December 2011
- ''Caenorhabditis remanei'' is a gonochoristic (male-female) species closely related to ''C. elegans'' (i.e., a fellow member of the Elegans gro Some earlier studies of non-''elegans'' species occasionally misidentified ''C. remanei'' as "''C. vulgaris''", or confused2 KB (229 words) - 15:56, 15 December 2011
- ...aenorhabditis_japonica. Unpublished preferably for Ensembl Pages for these species.162 bytes (19 words) - 15:31, 3 August 2023
- [[Category:Other species]]122 bytes (13 words) - 16:18, 15 December 2011
- [[Category:Other species]]119 bytes (13 words) - 16:19, 15 December 2011
- [[Category:Other species]]130 bytes (13 words) - 16:19, 15 December 2011
- [[Category:Other species]]123 bytes (13 words) - 16:19, 15 December 2011
- [[Category:Other species]]127 bytes (13 words) - 16:19, 15 December 2011
- [[Category:Other species]]117 bytes (13 words) - 16:20, 15 December 2011
- ...GAF files C. elegans specific? We have 39 expression annotations to other species (remanei, brenneri, brugia). ok to leave them out? If not, make sure that t ...ns? New GO GAF specifications have taxonID, so a single file with multiple species would be ok.3 KB (462 words) - 17:47, 4 February 2021
- Species UNIQUE ?Species1 KB (120 words) - 09:24, 10 August 2010
- The species model has been extended to contain more evidence and reference fields, whic * WS280 ?Species model additions925 bytes (145 words) - 14:56, 18 February 2021
- ...so benefit the project at the Alliance of Genome Resources for the 6 other species ...to human health such as..... Currently the majority of the data for these species is predicted data based on computational data such as InterPro2GO. We will2 KB (274 words) - 19:30, 21 August 2022
- Origin Species UNIQUE ?Species1 KB (129 words) - 09:51, 5 October 2010
- Species UNIQUE ?Species // added by krb 15/02/02 Species2 KB (193 words) - 14:28, 4 October 2010
- == GO::Species Annotation == It looks like we have ?Species objects for each of these bacteria, but4 KB (617 words) - 17:14, 23 January 2014
- pulling out the set of Live proteins for a given species, the added benefit of these tags is removed as the subclasses also gueries the species tag which slows it back up.2 KB (305 words) - 08:49, 5 October 2010
- == Updated species page == https://wormbase.org/species/all#0123--101 KB (229 words) - 16:05, 15 July 2021
- * species dependent - TH * TH - there are species with GFF3 only, nothing in ace2 KB (248 words) - 20:52, 27 March 2013
- ...se the ortholog info from ensemble compara we can immediately apply to 100 species -the blastP pipeline has only 8. Added Yanai's expression graphs for other species1 KB (164 words) - 17:33, 15 January 2015
- |Species | Species as an Ace::Object.2 KB (271 words) - 14:09, 19 June 2014
- Target_species UNIQUE ?Species Target_species UNIQUE ?Species1 KB (161 words) - 15:04, 1 November 2010
- Species UNIQUE ?Species // added by krb [021021]1 KB (119 words) - 16:43, 11 April 2013
- C. elegans current release [ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/gff/c_elegans.current.annotations.gff2.gz post-processed.gff2.gz] C. briggsae current release [ftp://ftp.wormbase.org/pub/wormbase/species/c_briggsae/gff/c_briggsae.current.annotations.gff2.gz post-processed.gff2.g8 KB (1,219 words) - 22:33, 24 October 2011
- == 5. SPELL for Tier II species == *RNA-seq data is becoming available for Tier II species2 KB (303 words) - 09:13, 5 October 2012
- Species ?Species #Evidence Added non-unique species connectivity so that papers can be sorted by species.2 KB (260 words) - 11:11, 27 July 2012
- Merged BLAST search for species with multiple BioProjects gbrowse feature request Under testing Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrow1 KB (160 words) - 14:45, 16 July 2013
- Species class ?Species3 KB (306 words) - 10:00, 26 October 2011
- // possibility to refer to other Intervals to describe a complex rearrangement Species UNIQUE ?Species3 KB (265 words) - 08:51, 5 October 2010
- ** options for species/bioproject ids disappear when you select blat * Dual display - species wiht mult bioproject ids1 KB (178 words) - 14:46, 9 July 2013
- * #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrow * #1511 - remove links to non-curated species strains1 KB (142 words) - 14:49, 3 September 2013
- * Gary feedback - will add species/strain/lifestage/etc... ** everything fine but tier II or III species991 bytes (135 words) - 14:55, 8 October 2013
- == 7. Discuss searching other species progress (Norie; 5 minutes) ==996 bytes (130 words) - 20:51, 29 September 2010
- *Oligo_set mapping as we do for other classes. *Addition of ?Species3 KB (475 words) - 14:53, 19 February 2013
- ''Caenorhabditis sp. 5'' is a member of the Elegans group of species, gonochoristic species, requiring mating between males and females for2 KB (301 words) - 09:54, 28 March 2017
- Species UNIQUE ?Species3 KB (223 words) - 09:22, 10 August 2010
- Origin Species UNIQUE ?Species2 KB (184 words) - 08:38, 17 August 2010
- ...ode known to serve as a vector for a bacterial disease of insects. The new species also exhibits heterogony.1 KB (185 words) - 16:04, 15 December 2011
- .... Draft complete genome sequences have been generated for several of these other nematodes, some of which are being curated by WormBase. For these organisms == Species Prefixes ==6 KB (977 words) - 19:43, 14 June 2011
- ***Do we want other filters? **For genes, the ace file contains ALL the gene objects in WB regardless of species.4 KB (600 words) - 18:40, 2 February 2022
- * other critical issues? == JD needs updated species file ==1 KB (199 words) - 15:33, 31 May 2013
- * Kimberly's Species tag in Paper model will be added for WS234 ...es and from there go directly to GBrowse, Blast..This is to make different species easily accessible.4 KB (503 words) - 08:30, 22 June 2012
- == [[Working Group:Handling Multiple Species|Handling Multiple Species]] ==2 KB (306 words) - 15:01, 14 January 2016
- ** Working on new species and updating config221 bytes (25 words) - 15:11, 17 December 2013
- ..., anti-rabbit antibodies, etc..). We have some papers, though that mention other nematodes with a low count (especially for phylogenetic studies) but might ...identifies those papers and populates a reference widget in WB for a given species (e.g. brenneri, japonica, pacificus, ..)?3 KB (490 words) - 17:22, 18 June 2020
- ''Caenorhabditis briggsae'' is a hermaphroditic species closely related to ''C. elegans'' (i.e., a fellow member of the Elegans gro [[Category:Other species]]2 KB (312 words) - 15:46, 15 December 2011
- **We needed seven new GO codes to incorporate PAINT and other external annotations. ...nce the GO annotations refer to a specific strain of these bacteria. Each species, and a sample PMID, are listed below:1 KB (199 words) - 19:08, 10 February 2014
- As the modENCODE DCC is overwhelmed with other work, she has proposed that WormBase make the data available to the public. ...to extract all our data from primary resources that can be referred to by other groups.5 KB (796 words) - 21:05, 10 March 2014
- *Note that we also run three scripts to populate species information for each abstract. ...es in the text of the abstracts, the other associates species based on the species information for associated genes (gin_species).3 KB (532 words) - 13:33, 31 March 2022
- * sequences for proteins and genomic features for all species except C.sp 5 and C.sp.11 ...een expanded to represent all species in wormbase (besides any of the "sp" species)2 KB (361 words) - 16:32, 17 October 2013
- ...Species UNIQUE ?Species //added by pad, as we are moving towards multi species readyness.4 KB (394 words) - 08:39, 16 September 2014
- == 3. Variation and RNASeq data from non-core species (Mary Ann) == sequence data from VW8 and LM (2 other isolates of M. hapla), as well4 KB (599 words) - 00:25, 4 May 2012
- | Species **[[Other nematodes|Other nematodes]]5 KB (641 words) - 08:30, 27 September 2010
- * #1511 - remove links to non-curated species strains * #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrow1 KB (188 words) - 14:50, 27 August 2013
- -species => <span><font color="#ff0000">'Caenorhabditis elegans'</font></span>,-g -species => <span><font color="#ff0000">'Caenorhabditis briggsae'</font></span>,-21 KB (2,963 words) - 18:18, 11 August 2010
- = SOPs for Getting Different Species GO Annotations into WB and GOC = ****IDs that correspond to non-elegans species, used for ISS annotations or the occasional annotation extension (column 85 KB (811 words) - 18:52, 3 November 2015
- ...date list of genomes in WormBase can be found at: http://www.wormbase.org/species/all **[[Other nematodes|Other nematodes]]662 bytes (82 words) - 15:07, 14 January 2016
- Add Species UNIQUE ?Species2 KB (294 words) - 16:14, 16 August 2012
- Species UNIQUE ?Species3 KB (252 words) - 16:46, 9 January 2014
- == Expr_pattern Species tag - Daniela == I would also like to add a Species tag in the Expr_pattern class5 KB (663 words) - 16:47, 5 December 2014
- ...the main function of handling the requests for the router, it initializes other views (those representing pages) and triggers the jQueryMobile's change pag = Browse Species View =4 KB (562 words) - 15:29, 19 June 2014
- ...as its siblings (Cho et al., 2004; Kiontke et al., 2004). Of these sibling species, three (''C. briggsae, C. remanei'', and C. sp. CB5161) have been isolated ...e Synteny Viewer gives an alignment of the ''zyg-1/bli-2'' cluster in both species.4 KB (705 words) - 20:02, 11 August 2010
- * organized by release and symlinks reorg access via species -- all files have name/version/content * allows addition of new species data for availability1 KB (182 words) - 20:41, 11 May 2011
- * WBPaper00046462 The recent discovery of a C. briggsae sister species, C. nigoni, has opened up the possibility of dissecting the genetic basis of HI in nematode species. However,3 KB (452 words) - 21:59, 20 March 2015
- ./wormbasegff2togff3.pl -gff elegansWSXXX.gff2 -species | gzip -c > elegansWSXXX.gff3.gz ...The script can handle both the C. elegans and C. briggsae GFF2 files. The species must be specified in command-line.2 KB (286 words) - 18:26, 11 August 2010
- *Discussion of literature pipeline for other nematodes **Which species?4 KB (641 words) - 15:23, 19 June 2012
- ***Aligned with other data in WormBase, timing needs to be calibrated *Discontinuity between species with regards to the data we capture4 KB (609 words) - 20:57, 3 November 2011
- Endogenous_in ?Species #Evidence Essential_for ?Species #Evidence6 KB (543 words) - 23:29, 15 March 2016
- == Upcoming Species == == Upcoming SPecies (MH) ==4 KB (629 words) - 16:57, 6 February 2014
- ..., I aligned them using PECAN and could not find the 2 introns in the other species. Therefore I propose that the form without the 2 introns is the ancestral o736 bytes (119 words) - 18:48, 17 August 2010
- Target_species UNIQUE ?Species Target_species UNIQUE ?Species3 KB (368 words) - 10:15, 1 February 2012
- ...nfererence pipelines, resulting in only limited integration with the other species in WormBase. If the gene models and other annotation have been deposited with an INSDC partner along with the genome5 KB (723 words) - 09:02, 22 May 2012
- All species summary: http://dev.wormbase.org:9010/species1 KB (213 words) - 22:01, 17 November 2010
- ** goes through config - dl image for each track/species * Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store [https://github.com3 KB (412 words) - 18:10, 23 July 2013
- ...9387}, and nine further draft assemblies of newly described Caenorhabditis species {PMID:1007946} * Ranjana: could do blog post about new species.2 KB (299 words) - 16:04, 20 May 2021
- * Some data exists in WormBase for non-elegans/non-WB-core species, like Brugia malayi and Onchocerca volvulus ...nclude concise descriptions and expression data for genes from these other species2 KB (384 words) - 20:25, 21 May 2015
- === Species in Postgres and ACEDB/Datomic === * Want to be sure that what gets dumped aligns with species loaded into ACEDB5 KB (880 words) - 15:40, 3 September 2020
- ...to comparisons between species; Raymond suggested a landing page for each species; more focused on the the "what" (data) rather than the "how" (UI) ...nical: trying to figure out organization and how to get contributions from other developers; current prototype is based on flatfiles in elastic search http:2 KB (306 words) - 16:32, 3 November 2016
- Add a Unique species field.436 bytes (59 words) - 13:03, 17 August 2012
- ''Caenorhabditis angaria'' (species 3) (PS1010, RGD1, RGD2) is associated with palm and sugarcane weevils, ''Rh ...familiar Elegans group containing C. elegans, C. briggsae, C. remanei, and other elegans look-alikes. Meanwhile, the genome of C. angaria (as determined by3 KB (437 words) - 16:02, 15 December 2011
- Species UNIQUE ?Species * Model proposal, including proposed changes to other classes, on [https://docs.google.com/document/d/19hP9r6BpPW3FSAeC_67FNyNq585 KB (705 words) - 16:31, 16 June 2020
- * #910 -Test GFF3 and update species still using Bio::DB::GFF to Bio::DB::SeqFeature::Store administration gbrow * #1511 - remove links to non-curated species strains2 KB (273 words) - 14:57, 10 September 2013
- ...Other_name ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names Species UNIQUE ?Species7 KB (712 words) - 10:40, 4 October 2010
- * Species -> autocomplete on species?2 KB (369 words) - 17:10, 25 May 2017
- ...the Picture dumper so that link outs to Article pages will go through DOI other than publisher's website. ** Example of a page with link outs here: /species/all/expr_pattern/Expr11339#012--10727 bytes (112 words) - 15:56, 19 October 2023
- Species UNIQUE ?Species // [020306 kj]4 KB (350 words) - 09:32, 17 June 2013
- ...der also evaluating pipeline on a small genomic region of ''C. briggsae''. Species-specific differences e.g. hexamer usage in CDS & exon/intron length may ...e/data/compara_ngasp.tar.bz2 COMPARA] databases (incl. a core database per species, orthologies, mlagan 3-way genomic alignments using WS160 vs latest ''brigg3 KB (454 words) - 18:54, 11 August 2010
- ...mBase. There are a few tracks in C. elegans that are not present in other species that haven't been added yet.2 KB (298 words) - 15:28, 23 December 2014
- Species UNIQUE ?Species3 KB (312 words) - 15:14, 15 July 2010
- ...DY OF EVOLUTIONARY BIOLOGY WITH CAENORHABDITIS ELEGANS AND CLOSELY RELATED SPECIES 24-26 MAY 2006, INSTITUTO GULBENKIAN DE CIæNCIA, OEIRAS, PORTUGAL FIRST ...rnational workshop dedicated to the study of evolution with Caenorhabditis species. The workshop will be held for three days from 24 to 26 of May 2006, at the2 KB (302 words) - 19:10, 10 August 2010
- ...ssues/6597 (Query from user about transcripts for a non WormBase parasitic species it would seem?)896 bytes (138 words) - 16:10, 6 September 2018
- === * Species/Sequence collection - Kevin === ...the assumption that there would only ever be one current assembly for each species.8 KB (1,073 words) - 15:31, 14 December 2012
- ...www.wormbook.org/toc_geneticsgenomics.html Biology and genome of nematodes other than C. elegans]''' ...[http://www.wormbook.org/toc_wormmethods.html Methods in nematode species other than ''C. elegans''] '''2 KB (225 words) - 14:23, 8 March 2012
- ** source/type changed for all species GFF2->GFF3 ** downloads newest versions of files for all species (go, gff, fasta, ace xml)2 KB (253 words) - 15:33, 6 September 2013
- ...ion could be displayed as the collection from Murray: https://wormbase.org/species/all/expr_pattern/Expr10431#012--10 ! Species (For primary papers, species are those for which experiments are reported; does not include sequence ali4 KB (572 words) - 17:01, 13 January 2021
- #[[Populating Species Tag]]1 KB (130 words) - 21:21, 15 March 2021
- -dsn => "dbi:mysql:database=".$self->species.";host=" . $host, my $species = $self->species;6 KB (980 words) - 18:48, 11 August 2010
- Species UNIQUE ?Species4 KB (410 words) - 17:08, 17 August 2010
- ...ates to curatable papers) mention both Caenorhabditis species and parasite species ...e species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton4 KB (646 words) - 17:33, 1 September 2016
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (717 words) - 18:20, 17 August 2010
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/gb2/gbrowse/ ! species4 KB (719 words) - 18:21, 17 August 2010
- ...p=sharing slides] (for Alliance) with a breakdown of technology over time, species represented (mostly human and mouse) ...al (data.humacellatlas.org) (only human and mouse; not interested in other species)3 KB (408 words) - 17:27, 17 December 2020
- Table name format: ''genus-initial''_''species''_''bioproject-id''_''release'' Table name format: ''genus-initial''_''species''_''bioproject-id''_''release''5 KB (723 words) - 19:36, 29 August 2013
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (738 words) - 18:20, 17 August 2010
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (723 words) - 18:21, 17 August 2010
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (723 words) - 18:21, 17 August 2010
- * Provide filter for orthologs via species784 bytes (103 words) - 17:46, 4 November 2009
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (725 words) - 18:20, 17 August 2010
- ...l/viral/whatever strain by following through from the Strain object to the Species. So, simply adding the Strain name here should be sufficient for the websit ...hould consider moving them out to be organism interaction tags, along with other organism relationship terms such as symbiotic, mutualistic, etc., afterall,15 KB (1,892 words) - 19:54, 10 February 2017
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (725 words) - 18:21, 17 August 2010
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (610 words) - 18:20, 17 August 2010
- my @tables = qw( wbgene humandoid paperexpmod dbexpmod species diseaserelevance paperdisrel dbdisrel ); #list of postgrestables, as dis_wb ...heHash{species}{$pgid}) { $species = $theHash{species}{$pgid}; } #will get species value10 KB (1,461 words) - 23:06, 27 February 2017
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/gb2/gbrowse/ ! species4 KB (735 words) - 18:22, 17 August 2010
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/gb2/gbrowse/ ! species4 KB (735 words) - 18:22, 17 August 2010
- *[http://biosci.umn.edu/CGC/strains/non.html Non-Caenorhabditis species]1 KB (209 words) - 21:14, 21 February 2011
- * Multiple facets/filters available to narrow down results, by object type, species, or topic * a Couple of other tickets are still open but people are working on them3 KB (421 words) - 16:39, 20 October 2016
- Species UNIQUE ?Species Species UNIQUE ?Species13 KB (1,341 words) - 20:12, 22 September 2015
- ...t pressing issue will be the standardization of GFF2 for Tier 1 and Tier 2 species. This (may) have an effect anywhere we extract a segment from GFF DB.''636 bytes (97 words) - 14:38, 17 May 2013
- | '''Species'''<br> | [ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/ WormBase]<br>11 KB (1,578 words) - 13:38, 10 April 2012
- - ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/geneIDs/ - ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/gene_ids/4 KB (689 words) - 11:13, 29 August 2013
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/ ! species4 KB (762 words) - 18:20, 17 August 2010
- == Other Items == * Was suggested that we use Other_name in ?Sequence_collection to store other name. ''nb. M.Tuli: I've just checked this and Other_name is not a tag in ?4 KB (597 words) - 18:34, 31 October 2012
- 2. Michael Paulini (using all WB nematode species)<br> There was a discussion of pathogen species objects.2 KB (358 words) - 14:03, 13 January 2014
- - Other MODs can also work on getting supplemental funding ...on adding new genomes/species to WormBase, including setting up Tier 1, 2 species. This discussion should be done in conjunction to WB's advisory board and m2 KB (370 words) - 16:18, 16 March 2023
- ** all species: gene, transcript, cds, protein, variation, phenotype, go_term, sequences d * also working on other WS237 issues1 KB (153 words) - 15:27, 26 April 2013
- *Is there a similar problem with other non-elegans/parasitic species? * Proposed that we should take one direction or the other3 KB (415 words) - 18:05, 22 October 2015
- - Issues with multiple strains (bioproject) from the same species are resolved. * they have own species index page, ftp links, gbrowse links3 KB (478 words) - 15:41, 23 February 2016
- * Populate them under "other names" * Species name should be suppressed when searching. Todd/web team will look into it.1,008 bytes (159 words) - 19:13, 15 December 2011
- * Current parasitic species in WormBase - should we "move" them into ParaSite? * Curation for parasitic species?8 KB (1,391 words) - 11:57, 6 August 2014
- | only if value is dead and species ~ elegans$ | Species9 KB (1,464 words) - 14:10, 29 May 2015
- ...body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates.1 KB (168 words) - 16:12, 15 December 2011
- 4. ''Choose a species.'' 4. ''Choose a species.''12 KB (1,838 words) - 18:16, 19 May 2015
- == IWM23 workshop - discuss online resources for worms other than C. elegans == ...to convince C. elegans researchers that now is the best time to adopt new species in their labs.4 KB (657 words) - 17:19, 15 June 2023
- * Common GAF was an impetus, but were other reasons * Some paper have both Caltech species as well as ParaSite species; this creates problems in the tool5 KB (715 words) - 15:49, 4 August 2016
- Other Changes: Revert Transgene phenotype-gene link but added to Phenotype_info hash. Added Species to Rearrangement6 KB (709 words) - 16:49, 21 December 2011
- === Adding Species information to nightly geneace dumps === ** Michael Paulini is adding Species information for the WBGene IDs in the genes.ace file8 KB (1,147 words) - 15:33, 7 May 2015
- ...s'' or the ''C. briggsae'' genome. Pick the species to be scanned from the Species menu. Species: "C. elegans"4 KB (687 words) - 19:56, 11 August 2010
- ...and pending nematode (re)sequencing projects. Please describe briefly the species, population or isolate you will be (re)sequencing, the technology you will :Get a strain other than CB4856 for SNP mapping, for behavioral (or other) phenotypes that cannot be mapped using CB4856.9 KB (1,382 words) - 17:55, 16 August 2010
- The closely related species ''Pristionchus maupasi'' and ''P. entomorphus'' naturally occur in close as [[Category:Other species]]4 KB (458 words) - 16:08, 15 December 2011
- * #1511 - remove links to non-curated species strains - JW == Other development ==3 KB (416 words) - 18:30, 24 September 2013
- * Karen will review the molecule curation with other curators at the IWM * 100 species, 922296 bioentity (protein, gene product ...)7 KB (1,010 words) - 17:08, 4 May 2017
- * Don't always shorten species to g_species - if not recognized, shorten to genus_species2 KB (222 words) - 15:42, 5 November 2013
- * How can we handle natural variation in C. elegans and other species? * How should we prioritize RNAi versus other gene function curation?4 KB (462 words) - 08:54, 8 October 2014
- *Include species tag? *Create an ontology of life stages for different species4 KB (695 words) - 15:26, 7 June 2012
- ...l_Model and one Disease_Relevance (and their related papers, databases and species); they will be grouped together in one instance of the Editor and grouped t Q:Updating: How do we update this obo file, how frequently do other obo files get updated? <br/ >14 KB (2,085 words) - 20:27, 7 July 2022
- ...6-D480). In their original form these consist of many different species-to-species pairs. For ease of use they have been consolidated into the following level ...ineage-specific expansions of paralogous proteins found solely in a single species such as C. elegans) and FOGs ('fuzzy' orthologous groups, such as zinc fing8 KB (1,256 words) - 00:26, 31 August 2010
- *Adding species information to ALL papers; can be one or more species per paper *Species information could be used to keep curation stats clear5 KB (689 words) - 15:35, 7 April 2016
- Refer to species list: ! taxonId !! species15 KB (2,088 words) - 16:16, 15 October 2020
- * Species -> autocomplete on species? -> mandatory What is listed as figure legend 1 should go into reagents- also other tech notes do not have the caption but only the descriptive text5 KB (800 words) - 18:29, 16 August 2017
- == Any Other Business == WormBase's All Species page (https://wormbase.org/species/all#0123--10-02) updated with new genomes from WB ParaSite release 165 KB (855 words) - 08:58, 8 October 2021
- * '''[[WB-ABM-2013-Agenda | Advisory Board Meeting]]''' wiki for agenda and other meeting details '''Wen - Other species Oligo set data, not in WS235.....is it planned for WS236? '''3 KB (564 words) - 17:27, 20 December 2012
- ...kout to insure that it is the most currently available configuration. The other items probably won't need to be changed ever but here's an explanation of t --species Name of species (should use same format as ALL_SPECIES.stats)15 KB (2,419 words) - 15:11, 26 July 2016
- * are there other data that should be announced or highlighted? (originator of the WormBreeder's Gazette among other things), his passing was announced yesterday, can/should something be poste1 KB (219 words) - 17:05, 18 February 2016
- ** Result was that all non-elegans species were build using old data ** In some cases, the frameshft/stop is conserved in other Caenorhabditis.5 KB (741 words) - 10:57, 21 August 2015
- ...sed, but I have discovered duplicate records caused by the addition of new species. The configuration has been updated, but a new build must be compiled. Un * bugs and other issues fixed along the way3 KB (456 words) - 15:50, 25 October 2013
- ** What about other nematode genes that are not characterized. When people do enrichment analys * Paper corpora for all species [MM & MZ]5 KB (787 words) - 18:10, 25 August 2022
- ...ld implement the Panther GO TE tool for both C. elegans and the other core species. (Jane Lomax) ...d to be the provider for gene association files, including parasites, core species, ig briggae, no extra work, interpro to go, phenotype to go, not from Tony,3 KB (539 words) - 10:56, 5 June 2015
- ...' other than Bristol, nematodes other than ''C. elegans'', or non-nematode species. | Genes studied or cloned||''C. elegans'' or other Caenorhabditis studied or newly identified in the paper.5 KB (816 words) - 20:11, 7 September 2011
- '''Names, Identifiers, Sequences, Species''' Species: Each gene can only be associated with one species.6 KB (847 words) - 23:51, 9 May 2023
- ...DB_info Database ?Database ?Database_field ?Text //for genes from non WB species Species_in_analysis ?Species XREF In_analysis //for recording the species used generate phylogenetic profiles, for WS24215 KB (1,645 words) - 18:54, 23 January 2014
- Primarily centered around the Species menu -> Resources ...for each species but they need help from others to look through all of the species and really identify the issues that remain to avoid confusing users.7 KB (1,182 words) - 13:50, 20 April 2012
- ...n rewrite the whole sequence pipeline. Can the Alliance team do it for all species?1 KB (229 words) - 16:31, 2 November 2023
- * species list issue: 14052 KB (244 words) - 15:52, 14 June 2013
- * Meloidogyne incognita genome added to WormBase as Tier III species * Paralog predictions added to Tier I/II species genes from wormbase-compara6 KB (711 words) - 16:31, 21 December 2011
- ...ludes the C. brenneri genome for the first time. Orthologies to the other species in WormBase have been determined and Gene names transferred from C. elegans Precalculated protein alignments are now made for each main WormBase species.6 KB (748 words) - 16:41, 21 December 2011
- ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/c_briggsae/PRJNA1073/c_briggsae.PRJNA10731.WS246.best_blastp_hits.txt.gz ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/species/c_briggsae/PRJNA10731/c_briggsae.PRJNA10731.WS246.xrefs.txt.gz14 KB (1,958 words) - 20:14, 2 January 2015
- * Kimberly/Paul - Species model additions > ?Species Evidence #Evidence // Meta data for why the object was creat3 KB (534 words) - 17:29, 1 October 2020
- ...cluster_summary_all_parallel.pl (downloads expression cluster data for all species) 5. For creating a report with all the numbers for each of the species, run15 KB (2,321 words) - 17:36, 18 August 2017
- Paper pipeline for other species *Kimberly will update pipeline to include papers from other species6 KB (983 words) - 18:02, 12 July 2012
- **species choose | Species9 KB (1,391 words) - 19:47, 19 April 2023
- ***enable the '''Homologs in Species''' filter and set to '''Caenorhabditis briggsae''',3 KB (348 words) - 10:42, 31 January 2013
- ...ld (as example, here: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/annotation ...y dumped into that one: ftp://ftp.wormbase.org/pub/wormbase/releases/WS243/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS243.best_blastp_hits.txt.gz2 KB (336 words) - 14:08, 27 August 2015
- Worm_disease_model ?Text ?Species #Evidence //added Jan 2014, for WS242 |7|| Species || Autocomplete dropdown || '''required''' || Homo sapien || ?Species || dit_species8 KB (1,088 words) - 22:59, 29 July 2016
- ! species3 KB (568 words) - 16:43, 17 February 2011
- *#Genome Sequences & Species (EBI/Hinxton)2 KB (256 words) - 17:36, 4 April 2013
- *Easy to use form, simple drop down menus to select, e.g., Species ...rgeted members of the community, get feedback; Who should we ask for other species?7 KB (1,047 words) - 15:34, 4 April 2013
- * will check all other species today1 KB (181 words) - 15:58, 20 September 2013
- * afp_othergenefunc (to capture gene function other than enzymatic activity) * Implications for gene descriptions, but what about other tools, applications at WB?7 KB (1,044 words) - 14:45, 8 October 2020
- * Other OA's may need to be updated accordingly ...ways to highlight potential orthologous/analogous components from relevant species6 KB (801 words) - 17:29, 2 July 2014
- wb_nematode.gpi.gz (all nematode species in WB) ...ired || 1 || 13 || taxon:6239 || n/a || NCBI taxonomy ID for corresponding species of entity in Column 2.5 KB (720 words) - 20:46, 10 October 2016
- Other issues: There are lots of other issues in the system not listed here, but will be worked on when time allow6 KB (909 words) - 21:56, 21 November 2013
- ===Species=== ...egans other than Bristol: ''' Data is present for ''C. elegans'' isolates other than Bristol, such as Hawaiian, CB4855, etc. Postgres character name: '''cn12 KB (1,832 words) - 18:43, 11 August 2010
- .... briggsae genome. Orthologies between C. briggsae and C. elegans and 'two-species sequence alignments' can be obtained using the Synteny Viewer under the 'Se The sequencing of three additional genomes of the Caenorhabditis species (CB5161, C. remanei and C. japonica) has been approved by the National Geno6 KB (914 words) - 15:39, 24 September 2007
- * Broaden scope to include all types of species-species interaction (?Interspecies_interaction class ???) ...consider how to make tag names that are unambiguous with respect to which species is playing a particular role8 KB (1,218 words) - 17:46, 2 April 2014
- * Can use text: "Compare with other model organisms at <AGR logo>" ** Links to AGR genes from C. elegans gene pages (not other species)2 KB (250 words) - 16:12, 19 October 2017
- *Should Juancarlos put postgres (and other) cgi's there? *Can this be of use for other nematode (other species) groups?7 KB (1,117 words) - 16:39, 4 August 2011
- ** 5 Caenorhabditis species === Species for genes in Postgres ===8 KB (1,120 words) - 16:19, 5 March 2015
- ...c-names. eg Ctr-dpy-10, Cni-dpy-18?<br> do we assign public names to other species? Should I tell the authors to not use them?2 KB (283 words) - 15:52, 3 August 2023
- ** Species entries, like "Acrobeloides butschlii wild isolate" or "C. briggsae" ** SObA? (Raymond); still working on multi-species SObA5 KB (747 words) - 16:31, 5 December 2019
- Visualization and other tools Find cross species data at the Alliance of Genome Resources2 KB (280 words) - 17:48, 1 April 2019
- search_species_change: search_species_change, // change the species search filter eg. [% dataTable_list(['Gene','Coding sequences','Species','Experiment'],fields.rnai.data.1.aaData,'table_rnai_1') %]6 KB (671 words) - 16:43, 20 August 2013
- **Queries can be saved and used again later (available to other users) ...n is to generate time-course expression data 'on-the-fly' later on so that other data sources can be compared and included in the same graph, given that the7 KB (1,074 words) - 17:19, 4 October 2012
- ...9387}, and nine further draft assemblies of newly described Caenorhabditis species {PMID:1007946} and replaced two C. remanei strains (PX356 and PX439) with a * Magda: Tell users about new data and new genome analysis. Species in compara are different. New orthologies, homologies.5 KB (794 words) - 16:30, 3 June 2021
- Input : Files staged at ${FTP}/releases/${RELEASE}/species Build nucleotide and protein BLAST databases for species with genomic sequence and conceptual translations. In addition, for C. eleg25 KB (3,632 words) - 03:11, 28 October 2013
- *Focus on genes in other species *Parasitic worm vs. Free-living worm descriptions (host, drugs, species-specific genes, etc.)9 KB (1,339 words) - 19:02, 31 January 2013
- **WormBook and other book chapters ...em as such in the curation form and marking them correctly, 3) determining species discussed in the no_curatable papers, etc.17 KB (2,401 words) - 22:36, 29 November 2017
- Origin Species UNIQUE ?Species8 KB (853 words) - 23:50, 16 April 2014
- | align="center" style="background:#f0f0f0;"|'''Species''' |||SPECIES:11 KB (1,688 words) - 11:06, 21 December 2011
- Species expression data from Itai Yanai *Importing pictures; potentially flagging each to a particular species10 KB (1,553 words) - 18:04, 7 February 2013
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/3 KB (489 words) - 18:14, 17 August 2010
- '''WormBase: a multi-species resource for nematode biology and genomics'''<br />[[User:Tharris|Todd W. H '''WormBase: a cross-species database for comparative genomics'''<br />[[User:Tharris|Todd W. Harris]],6 KB (781 words) - 02:18, 1 April 2012
- ...data (could discuss cross-referencing/linking between WB and WBPS for core species, cross-searching over the two resources, etc.) ...we should have a focus to the SAB meeting like collaborative efforts with other mods.4 KB (684 words) - 19:43, 5 December 2015
- ...matode genomics is present in WormBase, we are also accepting papers about other nematodes. ...l information available on the C. elegans gene but its ortholog in another species had been well studied. There are also papers used for earlier concise desc2 KB (352 words) - 18:13, 17 August 2010
- Per species:2 KB (307 words) - 14:04, 7 February 2013
- * WBBanner links (Species Resources Tools WBParasite) * Utilising the Species dropdown would be difficult as it would be cluttered, need to think of a cl4 KB (610 words) - 13:12, 14 November 2014
- ...es'', and ''Culex'') and humans, and is phylogenetically representative of other infectious nematodes. Infection of humans by ''B. malayi'' causes filariasi 7. [http://www.nematode.net/Species.Summaries/Brugia.malayi/index.php Genomic data] from the [http://www.nemato3 KB (383 words) - 16:15, 15 December 2011
- select all class gene where ->Species like "*elegans" and ->Status like "Dead"2 KB (329 words) - 15:21, 7 August 2014
- mkdir briggsae_20070200_CB25 [species]_[YEAR][MONTH][DAY]_[VERSION]2 KB (261 words) - 18:27, 11 August 2010
- *If you are interested in other species, find cross-species data at the Alliance --Ranjana4 KB (564 words) - 15:22, 4 April 2019
- *Species-by-species build processes?4 KB (612 words) - 17:13, 1 December 2011
- | Work with Template czar to get other necessary data for details | [[WormBase Model:Species|Species]]12 KB (1,559 words) - 18:14, 15 June 2011
- *Other contexts can be added later *Note: WOBr is going to be a widget on the Ontology Term page (all other ACEDB-based info will be present on page)10 KB (1,583 words) - 18:16, 5 February 2014
- *** can intelligently resolve paths containing species' bioproject id2 KB (226 words) - 15:32, 2 August 2013
- '''New Species'''1 KB (199 words) - 20:57, 3 November 2010
- ...55, 0, 0);">'''In particular, we have added additional databases for every species, and changed the way they are created (through the new update pipeline).'''4 KB (506 words) - 20:45, 10 August 2010
- species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) with the following files: ...BLASTX/ - This directory contains the blastx data for non-elegans species21 KB (2,346 words) - 11:15, 21 December 2011
- Interacting_species ?Species ?Strain3 KB (337 words) - 16:15, 19 February 2015
- |Are the GBrowsers for the various species working <br> http://dev.wormbase.org/db/seq/gbrowse/3 KB (530 words) - 18:14, 17 August 2010
