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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
- ...including statistics. Currently used for SVM curation, could be useful for other things too. * B.malayi will go into WS236 as core species (including a set of predicted operons)5 KB (752 words) - 18:55, 6 December 2012
- other synonyms were already accounted for in the .ace Same thing for othername, could go into synonyms and then dumped as other name.14 KB (2,213 words) - 19:26, 12 February 2019
- * Species agnostic, but tries to draw connections between human and C. elegans cell t * Marie-Anne Felix asked about species descriptions10 KB (1,475 words) - 16:57, 5 November 2015
- ...ed a technology catalog so that developers know what softwares are used by other MODs and they can work together. ...o more and more work for others (such as Textpresso ... ). Long term goal: Other MODs can help us with maintaining infrastructual so that web team staff can2 KB (339 words) - 18:43, 8 April 2016
- [[Category:Other species]]2 KB (324 words) - 19:34, 11 August 2010
- species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) ...a sub dir for each NCBI genome sequencing BioProject (BIOPROJECT) for the species, with the following files:16 KB (1,733 words) - 21:55, 11 May 2023
- ...ng problem with the parsing of the blat outputs where sequences from other species are aligned to a genome. Only a small fraction of hits are affected but th ...g to fix this asap but in the mean time if you are interested in any cross species alignments of transcript data in WormBase that look odd please double check6 KB (722 words) - 16:43, 21 December 2011
- ...phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel, Chris Mungall, Suzi Lewis, Nicole Washin ...o create configurations for all data types. Once C. elegans is done, other species will be easy. Nothing is difficult. It just takes time.5 KB (807 words) - 18:27, 4 September 2014
- // sequences from other species (e.g. targets of BLAT_NEMATODE) Species UNIQUE ?Species12 KB (1,258 words) - 09:29, 5 October 2010
- ...e graphic generated for protein homology like in the [https://wormbase.org/species/c_elegans/protein/CE28239#3--10 UNC-26, isoform a page] # Predicted Protein-Protein interactions from multiple species' orthology data in AGR2 KB (303 words) - 18:23, 16 April 2020
- ** Top-level species pages (/celegans, eg) and UI clues for distinguishing them3 KB (378 words) - 20:23, 2 March 2011
- ...t to adopt; few genetic model organisms, of those, FB has the most useful. Other mods use controlled vocabularies (CVs) that either are not comprehensive en ...n and analysis across diverse research communities and sources)for a cross-species genetic-based controlled vocabulary, I'll be submitting our terms to them,6 KB (982 words) - 15:33, 2 July 2015
- Since 'elegans' can refer to species other than ''Caenorhabditis elegans'' and since there are papers that mention ''C3 KB (403 words) - 16:02, 27 March 2019
- **Worm Phenotype ontology; attempt applying to other species? Some has been done already (e.g. C. briggsae) ***Benefit of curating phenotypes in other species? Particularly useful for genes not in C. elegans, for example12 KB (1,878 words) - 15:55, 6 September 2012
- *microPublication author tracking for all species ...raries - okay to just cite WormBase or should the user cite additional, or other, resources/publications?2 KB (325 words) - 15:24, 7 October 2021
- * Some immediate action items to deal with for expanding SObA to other ontologies and databases * People asking about essential genes in N2? Other strains? Other species? Junho Lee asked7 KB (1,062 words) - 14:41, 2 August 2018
- Build species: C.elegans2 KB (347 words) - 14:07, 2 July 2021
- * S.ratti will join the core species under the aegis of Jane Due by the end of next week (April 10th) for feedback from each other2 KB (334 words) - 09:04, 7 April 2015
- * request: Ability to share and edit other ppls templates #: add genus, species, and other name Intermine3 KB (451 words) - 20:13, 21 May 2013
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.16 KB (1,762 words) - 11:10, 21 December 2011
- *New GO annotation pipeline will bring in manual GO annotations made by other groups such as UniProt, IntAct, GO's RefGenome (PAINT) curators, UCL-BHF, e *Any objections? If so, other ideas?8 KB (1,246 words) - 15:52, 12 November 2013
- ...pecies? Can we port over the computed/derived descriptions for non-elegans species to the Alliance? ...red Data' (at least for the near term)? Or does it get integrated with all other expression data equally? Should discuss with Todd/Webteam5 KB (670 words) - 15:31, 3 June 2021
- species/ DIR - contains a sub dir for each WormBase species (G_SPECIES) ...a sub dir for each NCBI genome sequencing BioProject (BIOPROJECT) for the species, with the following files:17 KB (1,841 words) - 21:54, 11 May 2023
- * will be used as reference release for other sites (EG, etc.) * will show up on the Genome Browsers as a Tier III / non-core "species"2 KB (329 words) - 17:10, 6 August 2015
- 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 species15 KB (1,738 words) - 11:20, 21 December 2011
- * Textpresso: good to have a presentation for other MODs to show Textpresso capabilities? Yes. Maybe during sprint review * Secondary filter on papers with at least C. elegans as species9 KB (1,375 words) - 16:04, 18 April 2024
- === Flagging papers for species === * Going forward, Kimberly, Jane, and Michael will manually flag papers for species8 KB (1,224 words) - 15:34, 21 July 2016
- *1:45 More than just worms: cross-species data at the Alliance of Genome Resources. Chris Grove (5 mins)2 KB (306 words) - 08:41, 7 June 2019
- 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 species17 KB (1,950 words) - 09:37, 7 February 2012
- |||SPECIES: ...hange instructions to 'Please indicate if data for ''C. elegans'' isolates other than Bristol are presented in this paper."16 KB (2,310 words) - 11:05, 21 December 2011
- 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 species15 KB (1,653 words) - 10:13, 18 January 2013
- ** Worm Board (if active) or GSA could (help) organize; could expand into other domains ** SGD has good Alliance links; including the species hexagons3 KB (413 words) - 16:11, 6 October 2022
- ****Oligo_set mapping as we do for other classes. ****Addition of ?Species2 KB (383 words) - 11:59, 15 February 2013
- ...d to know species (usually OK for elegans, could be trickier for mammalian species) **Any others? Ask other WB curators.6 KB (901 words) - 19:21, 29 November 2011
- ...n the elegans gene and the non elegans gene required a correctly formatted species prefix e.g. "Cbr-". Formatting errors are not easily dealt with by automate (There may be also be other special characters with accents, umlauts, etc., The best thing to do would10 KB (1,696 words) - 17:21, 25 July 2013
- * <b>New species</b> ** Chip-seq and other large datasets - where should the be stored to maximise usage but cut overh5 KB (644 words) - 22:02, 23 January 2013
- Species: Species of origin. Other names: Names by which the gene may also have been referred (e.g., name assi7 KB (985 words) - 18:28, 17 August 2010
- * Example of a sequence feature connected to expression: https://wormbase.org/species/all/expr_pattern/Expr11278#02--10 ** Need Apollo to handle other species.9 KB (1,570 words) - 16:36, 21 September 2023
- ...we also import their coordinates and have a TransgeneOme track on JBrowse? Other than having the fosmids just connected to the construct class? In this way ...tting the next release ready and it will include variations from different species.3 KB (457 words) - 19:24, 7 July 2016
- <tr><td>Species</td><td>taxonomy()</td><td>"fields taxonomy"</td><td>taxonomy</td></tr>3 KB (485 words) - 15:37, 19 June 2014
- 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 species15 KB (1,729 words) - 14:15, 13 September 2012
- ...nclude universal groups (KOGs) found in all metazoa or all eukaryotes, two-species orthology groups (TWOGS) that are nevertheless ancient (e.g., orthologies f4 KB (621 words) - 15:38, 24 September 2007
- ...ecies/c_elegans/variation/WBVar02147646#02-4538-10 http://www.wormbase.org/species/c_elegans/variation/WBVar02145299#0657942--103 KB (423 words) - 16:35, 7 September 2017
- |||SPECIES: ...Bristol||cnonbristol ||Please indicate if data for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.||13 KB (1,960 words) - 11:07, 21 December 2011
- * issues around non-elegans species3 KB (454 words) - 18:36, 10 July 2023
- | :address.other-phone/type | :analysis/species-in-analysis35 KB (4,174 words) - 10:52, 2 February 2015
- ...arching "WNT4", then choosing category "Gene Ontology" provides facets for species * Question is: how are these species associated to the GO terms?8 KB (1,289 words) - 18:11, 10 November 2016
- * Adding 2 new species to WS2292 KB (346 words) - 21:47, 7 December 2011
- ** Species-species interactions versus more specific strain-strain interactions ** Should we create topics that represent species-species interactions that can then be associated to relevant strain-strain interact10 KB (1,485 words) - 18:08, 5 March 2014
- ...ers from the author first pass form sent out to authors of publications in other journals; although all the datatypes on the form are the same, the JFP high ***currently only elegans alleles; priority on curating alleles of other species is very low17 KB (2,790 words) - 20:50, 10 January 2017
- * What new tools or features should we be working on? What do other sites have that we don't? * This has implications for comparative analysis of species available in ParaSite2 KB (379 words) - 16:39, 1 October 2015
- Other Changes: ?Gene Orthologue_other ?Database ?Database_field UNIQUE ?Accession_number ?Species #Evidence8 KB (787 words) - 10:56, 21 December 2011
- ** Separately, other things we talked about were: ** Which papers don't get into Alliance, do we want a species filter (will come up tomorrow)3 KB (492 words) - 18:48, 17 March 2021
- incorporation of (many) other genomes. This model need further consideration. Other classes should also be reviewed.7 KB (1,220 words) - 15:50, 25 November 2011
- Brugia malayi is also updated as a "genome browser" only species in this release. Other Changes:6 KB (680 words) - 07:37, 11 January 2008
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.17 KB (1,758 words) - 16:47, 21 December 2011
- ...n and tissue expression information for unknown genes in multiple nematode species.4 KB (406 words) - 18:13, 25 April 2023
- * Gary W. has started working out a similar display for all species3 KB (448 words) - 16:04, 5 October 2017
- ...G (Proline)-antocodon tRNA in C. elegans. This is known (and true for many species).3 KB (405 words) - 13:18, 15 January 2016
- Choose species; downloads fast, gff3, GO, gene association files, classes for XML2 KB (357 words) - 15:40, 30 August 2013
- ** Plan to update all tier2 species for WS250 ** Some species (e.g. P. pac) have few/no gene model changes, but could do with being broug11 KB (1,714 words) - 11:04, 27 July 2015
- Other Text // added to catch all clones 011017 dl 5548 Other elegans cosmids10 KB (1,176 words) - 22:24, 18 March 2014
- ** can we mine author data from other sources (institution, laboratory); important to get laboratory address for * Cross-species comparison of developmental gene expression10 KB (1,453 words) - 18:52, 4 February 2015
- ...interactor PCR_non_directional_interactor UNIQUE ?PCR_product XREF to? ?Species ...Sequence_non_directional_interactor UNIQUE ?Sequence XREF to? ?Species50 KB (5,228 words) - 15:10, 21 July 2017
- |||||colspan="6"|SPECIES: ...field'''|| cnonbristol ||Check if data for ''C. elegans'' natural isolates other than N2 (Bristol) are reported.''e.g. Hawaiian, CB4855, CB4852, CB4507, LSJ17 KB (2,417 words) - 11:04, 21 December 2011
- ...will prove to be successful, we will scale it up to include submission of other scientific findings (laser ablation experiments, rnai experiments..). *species -> Select your species dropdown on species21 KB (3,194 words) - 02:08, 17 May 2018
- ...pdates of WB and Alliance, Community curation efforts--Acknowledge system, other forms?, MicroPublication (?), JBrowse, and any tool updates? anything else? ...k (use case starting with WB, going to Alliance for more details and cross-species comparisons)3 KB (503 words) - 21:00, 6 January 2023
- *Raymond will soon be getting other ontology info into the browser ...tion would be best while curating a paper; update on WikiPathways site for other curators to see13 KB (1,983 words) - 16:40, 7 November 2013
- - We could add these 18 new genomes in as tier 3 species - gene trees / synteny would probably be the most useful views, keeping in ...ant to display the SVs as tracks on N2 rather than bringing them in as new species for WB.7 KB (1,107 words) - 16:19, 20 April 2023
- ** Migrate a subset of papers for a defined list of species? ** Some of our non-C. elegans papers may be included in other groups' corpora3 KB (487 words) - 16:36, 18 March 2021
- ...nclusion or exclusion of 5' and 3' flanking sequences, and RNAi phenotype. Other data sets can be filtered in analogous ways. Moreoever, WormMart allows mor3 KB (545 words) - 19:45, 11 August 2010
- **Non-C.elegans species **Export pipelines for other species?9 KB (1,302 words) - 16:38, 2 June 2011
- ...for their WB lab page. To track who is a PI for which Lab. To connect to other Persons for Intellectual Lineage. Connect authors to Persons so Papers hav ...etimes done by region / country, but this is rare. If anyone can think of other use cases for person data, please let us know. While we mostly only use the10 KB (1,547 words) - 21:31, 2 January 2024
- Sentences that refer to proteins or gene products from other species were left blank, but could be classified with the same criteria as for C. e **False positive sentences include statements of other types of experimental data and statements from Materials and Methods. Some8 KB (1,272 words) - 21:49, 19 December 2012
- ...port the whole human and mouse canonical gene sets to facilitate this (and other things)? ...ed a ticket to develop linking to this data as don't want it as a WormBase species.3 KB (450 words) - 16:07, 7 August 2014
- Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence32 KB (3,649 words) - 20:55, 21 May 2020
- 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 species15 KB (1,708 words) - 10:14, 18 January 2013
- ...atment and control. H. contortus is a close relative of the human hookworm species and belongs to the nearest phylogenetic group of parasites to the free-livi ...of wet grass and wait to be ingested by a grazing animal. Sheep, goats and other ruminants become infected when they graze and eat grasses containing the L33 KB (493 words) - 16:03, 15 December 2011
- *** RNAi mapping (review of mapping pipeline and extension to other species)3 KB (438 words) - 07:19, 6 October 2014
- ...s not having C, and C not being very informative. We're already combining other fields like phenotype IDs + labels.3 KB (496 words) - 16:06, 6 August 2020
- ...etter functional description of uncurated genes (especially of non elegans species). ...atabase URL links and what is the new technology for making these links to other websites?3 KB (452 words) - 17:48, 7 March 2013
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.15 KB (1,647 words) - 10:06, 22 December 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 species14 KB (1,572 words) - 10:37, 11 November 2011
- Once a gene has been selected (or typed in), an "RNAi reagent" field and a "Species" field will appear: ...out in several species, the form has a species selection to specify which species the RNAi experiment(s) was/were carried out in, with a default to Caenorhab26 KB (4,016 words) - 21:32, 8 April 2020
- 1) One way to go is to link the expression to the sequence, other than the gene. From the Expr_pattern model: ...e where is the boundary between artificial and endogenous expression if no other experimental evidences -IHC, ish- are available.24 KB (3,538 words) - 17:50, 15 December 2015
- for example, that issues of species designation, nomenclature, experimental details are3 KB (564 words) - 19:15, 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 species17 KB (2,002 words) - 14:17, 13 September 2012
- Transgenes are also entered by other curators in the course of curating Expression pattern (Daniela), Gene Regul * Remark "Other integration method: ..."9 KB (1,321 words) - 21:59, 3 May 2020
- ...) it is not easy to switch between the sites to access data the respective other is missing * Paul S - Are people happy with WormMethod chapters, have people looked at other people's ?3 KB (558 words) - 17:29, 7 May 2015
- **#Genomic data (data related to species, assemblies, gene model curation etc) ...s (please correct me if that's not what you said) Karen mentioned we have other sources for minting DOIs if Mike Cherry's 50k/year are not enough. Magda s3 KB (511 words) - 18:54, 18 February 2021
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.16 KB (1,674 words) - 11:38, 20 April 2011
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.15 KB (1,610 words) - 11:20, 21 December 2011
- And for species specific-data /usr/local/wormbase/intermine/data/WSVERSION/SOURCE/SPECIES/DATA_TYPE9 KB (1,231 words) - 14:55, 19 June 2014
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.15 KB (1,583 words) - 11:13, 21 December 2011
- genomes DIR - contains a sub dir for each WormBase species with sequences/protein - WormBase protein set for species + history etc.15 KB (1,756 words) - 11:21, 21 December 2011
- * discordant feature names in Ace and GFF for (at least some) Tier III species Presentations and other meeting info in this folder4 KB (576 words) - 16:28, 17 June 2021
- genomes DIR - contains a sub dir for each WormBase species with sequence, gff, and agp data sequences/protein - WormBase protein set for species + history etc.15 KB (1,622 words) - 11:11, 21 December 2011
- *[[WormBase_Genomes| Overview of species' genomes available in WormBase]]5 KB (646 words) - 17:11, 25 November 2020
- species.tt2 [% PROCESS "shared/fields/species.tt2" %]5 KB (687 words) - 14:10, 19 June 2014
- 2) nematode EST sequences of species not represented in WormBase were updated for BLAT from EMBL release 91. Other Changes:7 KB (831 words) - 07:36, 11 January 2008
- ...but will mark as functional annotation so that it doesn't filter into any other pipelines This table has been created to record the taxon ID of the nematode species studied in the paper.25 KB (3,238 words) - 16:42, 8 November 2019
- * Species-specific proteins: how best to find them? HMMs (Jackhammer)? ** There is still a strong need for cross-species variant mapping/visualization8 KB (1,121 words) - 14:01, 15 July 2019
- 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 species17 KB (1,988 words) - 11:15, 21 December 2011
- translated_nucleotide_match:BLAT_NEMATODE (ID,Target,species) translated_nucleotide_match:BLAT_NEMBASE (ID,Target,species)19 KB (1,985 words) - 23:13, 13 August 2010
- :cell/other-name (919 values, 0 evidence -- Raymond suggests killing this class?) :cell-group/other-name (25 values, 0 evidence)7 KB (604 words) - 18:21, 11 November 2014
- 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 species16 KB (1,820 words) - 14:15, 13 September 2012
- * Underscore.js for templating and other utilities |-- Browse Species View5 KB (769 words) - 15:16, 19 June 2014
- ...Currently, these files contain all members of a given class, regardless of species. ...e (see above) is more recent than the latest timestamp in gin_molname. In other words, if WS is more recent than the postgres timestamp, the tables are upd18 KB (2,743 words) - 17:14, 16 March 2023
- | AceDB class that details display etc. of objects in the other classes | [[WormBase Model:Species|Species]]16 KB (2,207 words) - 23:06, 9 January 2014
- ...ments, as found in the literature pertaining to ''C. elegans'' and related species. There are some important things to consider when curating RNAi experiments Species UNIQUE ?Species29 KB (4,152 words) - 20:29, 30 July 2019
- ** We will ask other MODs and UniProt about how they deal with this issue ** Can we identify genes other than C. elegans/worm? Are not doing now, and will stick to C. elegans for n9 KB (1,368 words) - 15:27, 4 October 2018
- Wen, treat as any other GFP expression pattern, image data for individual reporter. homol_homol tag what about other curation data? <br>4 KB (709 words) - 13:27, 5 April 2021
- ==WormBase - manual annotation, cross-species complementation assay==17 KB (2,104 words) - 22:44, 17 December 2014
- * Information poor genes can take advantage of information across MODs/species ** Each gene will become a single Noctua model; not linked to each other initially9 KB (1,364 words) - 15:39, 7 February 2019
- ...Prototype 2 as a default view; we could possibly have a toggle to see the other view *** A link to Textpresso could be done regardless of other approaches; low-hanging fruit?13 KB (2,025 words) - 16:28, 7 November 2019
- ...japonica</i><li><i>C. remanei</i><li><i>Brugia malayi</i></ul><p>All other species in WormBase have their gene annotation imported from the authors or are pre ...sion names <b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of cont56 KB (9,514 words) - 09:48, 23 October 2015
- ...japonica</i><li><i>C. remanei</i><li><i>Brugia malayi</i></ul><p>All other species in WormBase have their gene annotation imported from the authors or are pre ...sion names <b>AscSuum_1.0</b> and <b>ASU_2.0</b></p><p>The genomes of most species in WormBase are incompletely assembled, being left as various sizes of cont56 KB (9,520 words) - 11:51, 21 October 2015
- * We could make different species entries that specify the assembly version4 KB (605 words) - 15:21, 3 March 2020
- === Other C. elegans genes implicated in UPR === We will review the gene-models and naming of the genes in our non-core species (C.briggsae / C.remanei / C.brenneri / C.japonica / B.malayi).10 KB (1,194 words) - 16:35, 13 December 2013
- * Generates generic per-class XML dumps for each species in <code>model</code>. The files generated will reflect the ace queries used to generate them. All species are loaded unless otherwise specified.25 KB (3,652 words) - 23:06, 25 December 2014
- ===Other related pages=== |'''''C. elegans'' other than Bristol'''|| cnonbristol ||afp,cfp||none||NC||6 KB (841 words) - 08:24, 24 October 2014
- ** Species based SVM? Currently use string matching to derive different corpora ** Finding genes and determining which species those genes belong to?8 KB (1,228 words) - 20:57, 14 July 2020
- *Make Tier II & III species more accessible **Bob Waterston's group has sequenced several strains, no other N2s in the world have alleles they have4 KB (617 words) - 17:01, 19 July 2012
- ...at add new knowledge, or validate existing knowledge from studies in other species or experimental systems (eg., cell culture, etc.).5 KB (782 words) - 20:56, 8 January 2020
- * what are the other sessions going to look like? ** please test new species/new genome browser tracks4 KB (624 words) - 17:15, 4 April 2013
- ...d have MODs move DBs to central architecture, but not integrated with each other. ** WormBase curates to datatypes, most other MODs curate all data per paper.4 KB (743 words) - 12:22, 5 March 2021
- * This pipeline will be added once other features (i.e. topic filtering) have been sorted out ...lone tool (CGI) to allow curators to convert paper IDs to WBPaper IDs from other paper ID formats (e.g. PMID, DOI, etc.) (Actually, it'll be a new function10 KB (1,664 words) - 17:02, 4 December 2013
- * based on a reference image set (one image per species, per track, per example landmark)8 KB (936 words) - 18:39, 18 June 2014
- ...s, anatomy terms, disease relevance, signaling pathways, phenotypes or any other categorical distinction we see as appropriate as we investigate this organi *Ecology of ''Caenorhabditis'' species10 KB (1,279 words) - 18:20, 18 October 2013
- Other Changes: Paralog ?Gene XREF Paralog ?Species #Evidence //mh6 for adding paralogs6 KB (662 words) - 16:50, 21 December 2011
- ** Are species-specific anatomy ontologies being utilized for expression annotations or st * If so, do we need to have a more general approach/strategy other than creating new folders in the individual curator directories?5 KB (670 words) - 16:00, 5 August 2021
- #'''Disease of Species (dis_species)''' #*Auto-complete drop-down with controlled vocabulary of species list36 KB (4,595 words) - 18:10, 15 March 2023
- Worm_disease_model ?Text ?Species #Evidence ...tering genes such as the rRNAs and act-123, but can definitely be used for other functions. Currently this is not displayed on the site7 KB (881 words) - 15:46, 21 November 2013
- *Citation -> the citation will be generated as the other brief citations for papers are generated and will be stored in Brief citati *DOIs will be handled as other Paper DOIs are handled -might be formalized (DB_info as per Raymond's sugge7 KB (934 words) - 19:56, 27 September 2016
- ...lts by Dataset Tags" to filter the results based on their experiment type, species, tissue specificity, and biological processes. ...these per-dataset weights, weighted correlations are calculated for every other gene in the genome to the query set. In this way genes that agree with the6 KB (964 words) - 18:49, 22 May 2018
- * Sequence curation update – other worms including parasitic nematodes/ How we prioritize with all the new seq * Talks by other advisors5 KB (763 words) - 00:51, 19 September 2014
- ***'''what other fields ? no app_name ? you for app_curator ? -- J''' ...n app_term ?''' yes, sorry<br> '''This implies they can't be blank for other stuff, the script only does some stuff for pgids with data in app_term, doe23 KB (3,334 words) - 19:01, 31 October 2017
- Other Changes: species. These will be populated with data in the future as more6 KB (763 words) - 10:43, 21 December 2011
- Other Changes: If you require a complete database with all data for each species you will have to6 KB (766 words) - 16:38, 21 December 2011
- * Added RNAseq FPKM download function for 9 species: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/fpkmmine.cgi * Include other papers in need of curation at bottom of email; possibly, would it turn off5 KB (818 words) - 15:55, 1 November 2018
- ...maller than what we started off with. Platform should have ability so that other ppl can write application on top of this platform ...y - rare biosphere - really long tail of distribution of species. Very few species out there we can see. Others barely exist - still there, still exchanging g15 KB (2,658 words) - 19:16, 11 April 2014
- 4) The Phenotype Ontology has been modified to curate nematode species other than the C. elegans \u201cN2\u201d strain. This includes a change in term n Other Changes:6 KB (770 words) - 11:06, 21 December 2011
- ...ba alignments have been remade based on the chromosomal sequences for each species Other Changes:7 KB (771 words) - 10:52, 21 December 2011
- | Other_name||abp_other_name||bigtext||Other Name||all|||||||| | Other_animal||abp_other_animal||bigtext||Other Animal||all||||||||37 KB (5,333 words) - 19:07, 27 June 2019
- ...d (or not_observed), Gene Regulation objects, Genetic Interaction objects, species, and general remarks about the experiment. If you need to add other information pertaining to the phenotype, such as penetrance, quantification47 KB (7,989 words) - 23:40, 1 September 2015
- *Five new species *Working with other MODs5 KB (843 words) - 17:26, 1 November 2012
- ...al well location, WB ?Clone object), Strain AND Genotype, Delivery method, Species, and Phenotype ** Very difficult/frustrating to find orthologs from other organisms5 KB (843 words) - 16:32, 4 December 2014
- We don't too much with ontology other than display a list of associations for a given object. What else can we d * show other genes with similar (aggregate) gene ontology6 KB (842 words) - 17:01, 21 October 2011
- ...patched for WS194<br><br><br>Known Problems:<br>---------------<br><br><br>Other Changes:<br>--------------<br><br>Proposed Changes / Forthcoming Data:<br>- ...should correct the ids, merge them into the C.elegans proteins and fix the Species + EnsEMBL xrefs11 KB (1,614 words) - 16:52, 21 December 2011
- Other Changes: Ortholog_other  ?Database ?Database_field ?Accession_number ?Species #Evidence8 KB (820 words) - 10:51, 21 December 2011
- 2) Simple Species additions for papers and provenance (Kimberly/Paul) *What do other MODs have? Think about in terms of Alliance5 KB (890 words) - 18:36, 5 November 2020
- * Could the phenotype form be adapted for other species? Possibly but depends on:6 KB (903 words) - 15:28, 2 April 2020
- Transcript alignment data from non C.elegans Caenorhabditis species (C.briggsae / C. brenneri / C.remanei / C.japonica) to the C.elegans genome Other Changes:9 KB (819 words) - 10:53, 21 December 2011
- * SObA for other species, we need to assess interest6 KB (910 words) - 16:43, 7 March 2019
- ...ons that we never required an explicit Y/N for every field and flagging by other methods, at least in some cases, suggests authors were not thorough ** Other meetings36 KB (4,994 words) - 17:27, 14 February 2024
- ...directory is 'gene_lists' under ~/release/<WSXXX>/<species>/ for all nine species #Obtain the complete list of gene names and IDs from postgres for the nine species, only gene Ids (gin_wbgene) and gene names (gin_locus) are used65 KB (9,380 words) - 22:39, 5 July 2018
- *Other species6 KB (944 words) - 16:25, 1 November 2012
- ...we used for innate immunity analysis and used by many researchers studying other things using microbial data as markers for cancer and other chronic diseases29 KB (4,082 words) - 19:15, 11 April 2014
- ...ure. Internet access through Harvard guest. They won't allow you to access other ways. *** Did you come across data for other curators23 KB (3,248 words) - 12:58, 22 September 2014
- ...e”) and then to individual BLAST matches with highly similar proteins in other organisms. Diagramming all of these allows the user to quickly see what par ...nd ''C. briggsae''.''' Here the ''zyg-1'' loci from two ''Caenorhabditis'' species are shown in syntenic alignment, making their precise similarities and diff19 KB (3,061 words) - 23:01, 13 August 2010
- ** Brief statement on curation of other nematode species * Tazendra, Mangolassi, Athena, Canopus, other Linux machines backed up6 KB (857 words) - 16:01, 2 October 2014
- OTHER Species UNIQUE ?Species20 KB (2,339 words) - 18:04, 23 September 2015
- ...ipt'''||'''Ontologies used'''||'''Other dependencies'''||'''Curator'''||'''Other remarks''' ...tables are obo_data_<datatype>, obo_syn_<datatype> or obo_name_<datatype>. Other OA datatype tables include trp_<tables>, mop_, grg_, abp_. Exceptions are20 KB (3,050 words) - 21:01, 19 April 2017
- ...ancarlos.wormbase.org as cost/benefit analysis is unfavourable to consider other options. * Further developments being made on Noctua and other LEGO software6 KB (906 words) - 21:38, 30 September 2015
- ''Other process related pages''<br> * List of processes based on WormBook and other reviews. Mined through GO hierarchy20 KB (3,088 words) - 19:17, 13 August 2020
- ...ts observed in skin, eye, brain, viscera, palate, tongue and other tisses. Other mutations ...onto human proteins, rather than other way around - keep in sync with with other projects, also limits sentence to a subset of isoforms?36 KB (5,076 words) - 01:38, 2 March 2016
- *1) Transfer info from elegans to other species *Annotation on tablets, other mobile devices? Read only?7 KB (1,123 words) - 16:39, 6 December 2012
- link outs to other databases ...e do provide access to bacteria, pathways vis tools, image analysis tools, species comparison tools. show model org pathway side by side.31 KB (4,384 words) - 19:08, 11 April 2014
- ** How can we work with other MODs on curation strategy? ** Other species8 KB (1,130 words) - 13:27, 4 February 2016
- channels (can be one of ZVI, DIC, GREEN, RED, BLUE, OTHER). The channel need to have same resolutions. Generally all entities in our * different species in TRG DB (request parameter)11 KB (1,190 words) - 19:16, 26 September 2019
- .../blob/master/ingest/expression/wildtypeExpressionModelAnnotation.json (and other specs) must be a publication, as defined by the publicationRef.json https:/ ** Are personal communications used in other classes?9 KB (1,377 words) - 16:36, 4 March 2021
- * Worm data in SPELL may be more complicated than the yeast data (different species, platforms, meta data, etc.)8 KB (1,189 words) - 14:10, 5 July 2018
- *oogenesis (non-species specific term)(2004) **Interacting_strain and Interacting_species: for capturing the strain or species when dual-taxon GO annotations are made, for example, to annotate gene prod30 KB (3,904 words) - 18:45, 13 May 2020
- ...of predictions that will be used to form the canonical gene sets for each species are available on the [http://ftp.wormbase.org/nGASP/final_gene_predictions/10 KB (1,177 words) - 17:54, 16 August 2010
- **Web redesign meetings on Thursdays will have to be every other week? Do both same day? **break physical interactions away from other interaction types?8 KB (1,282 words) - 17:08, 7 July 2011
- New genome assemblies and gene names across species8 KB (1,161 words) - 16:34, 7 March 2013
- * other names for the transgene reported by different authors Species UNIQUE ?Species29 KB (4,575 words) - 16:23, 3 March 2022
- Other Changes: Added NBCI tax id to ?Species19 KB (1,735 words) - 11:07, 21 December 2011
- use term - identify association with other terms ...the metabolic reconstruction two commercially utilized probiotic bacterial species. Aided by metabolic network models we will discuss initial results of ge- n25 KB (3,541 words) - 19:14, 11 April 2014
- ...Other_name ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names < Species UNIQUE ?Species235 KB (23,325 words) - 10:33, 3 July 2014
- * Do we want to start working on summaries for other entities, like variations? * Many genes (120+) have primary names that are also secondary names of other genes8 KB (1,262 words) - 15:34, 3 May 2018
- * Make questions about species higher profile.9 KB (1,431 words) - 23:32, 23 June 2015
- ...at have been shown to effect the biology of the worm. We provide links to other databases that deal with these molecule entities in greater detail. ...nction, protein interaction, cellular processing, biochemical pathways, or other chemical interactions." (from [http://www.nlm.nih.gov/cgi/mesh/2009/MB_cgi?50 KB (6,966 words) - 19:15, 13 August 2020
- ...display expression data that we do not (or cannot) update differently from other data * Other strains have been added via direct communication with Mary Ann9 KB (1,490 words) - 15:35, 6 October 2016
- **For example, RO also has terms from other ontologies: ...g is itself part of that thing. Two distinct things cannot be part of each other." xsd:string11 KB (1,898 words) - 16:43, 7 June 2018
- ...w is AGR disease data display compared to WB/MODs? WB is generally (as are other MODs) ahead of AGR * What do other MODs do? How extensive is the outreach to the community?10 KB (1,586 words) - 15:30, 2 November 2017
- ...that have some allele format (?) Yes, these must be gene names from other species that have a phenotype, but are not cloned and therefore the name isn't mapp12 KB (1,973 words) - 20:53, 16 June 2011
- ...d in elegans, and subsequent annotations will be useful for propagation to other nematode genomes. ...ist, but may not be the only relevant publication, so we may need to check other papers for writing a complete description.47 KB (6,852 words) - 04:27, 8 December 2020
- ** Still lacking other tools for microarray and RNA-Seq data * Chris Mungall: mapping phenotypes across species10 KB (1,474 words) - 15:54, 30 April 2014
- Species UNIQUE ?Species ...248 we have 19052 objects coming from Yanai elegans; 68097 for Yanai other species, 10545 for Miller tiling arrays and 13877 manually curated -> 111571 total104 KB (15,303 words) - 19:39, 11 May 2023
- **[http://dev.wormbase.org:8023/species/c_elegans/interaction/WBInteraction000505644#023--10 WBInteraction000505644 **[http://dev.wormbase.org:8023/species/c_elegans/gene/WBGene00018788#8--10 WBGene00018788]29 KB (4,254 words) - 20:25, 27 April 2012
- * Will need to think about how genotypes are built and stored at other MODs ...ly throughout a paper when applicable, but would likely not be used in any other papers (we would likely accumulate redundant objects in the DB)12 KB (1,930 words) - 17:12, 1 February 2018
- ** Daniela to check in with the Alliance to see what the other groups are doing ** Predicted (physical) interactions: Interologs, Inter-species extrapolations11 KB (1,703 words) - 15:27, 5 April 2018
- * Print list of WormBase tools or user guide on cloth (one side; logo on the other?)? * GEO forms apply to all species; controlled vocabularies/ontologies could be submitted to GEO for incorpora11 KB (1,676 words) - 15:28, 2 May 2019
- ....g., WB's 'functional annotation papers' or TAIR's black list of papers on other organisms - Tanya sent me a list of 1243 papers like this) or restricting s This box lists all entities within the species-specific protein or gene tag. Right now, the category name for this will b17 KB (2,749 words) - 20:04, 21 January 2011
- ...developed by Lincoln Stein for the GMOD consortium and is widely used for other model organisms. It allows users to browse through the whole genome for fea ...r WormBase groups, and so a lot of data pertaining to gene predictions and other features annotated on to the genome are created and maintained by those gro67 KB (10,954 words) - 09:22, 19 February 2013
- ...n aligned to orthologous sites in the genome of ''C. briggsae'', a sibling species of ''C. elegans'' (Stein et al., 2003). Finally, there are an increasing nu '''''Using other web sites relevant to C. elegans'''''30 KB (4,765 words) - 20:03, 11 August 2010
- * Do other MODs use ECO? * Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria14 KB (2,226 words) - 15:31, 7 June 2018
- ...ink for users to make comments or ask questions to the WormBase staff, and other links to WormBase policies on copyright and privacy; these links are given ...lowing protocols are intended to be illustrative, but not exhaustive; many other searches are possible.103 KB (16,375 words) - 23:39, 30 November 2010
- **Don't forget the species file .txt file! ...lable here: ftp://ftp.ebi.ac.uk/pub/databases/reference_proteomes/QfO/). Other issues (e.g., pseudogenes still represented as proteins in UniProt), will h23 KB (3,744 words) - 15:12, 23 December 2022
- ...nd elegans-current_release symlinks point to the current releases for both species.34 KB (5,450 words) - 18:24, 17 August 2010
- ...fer bit of file simultaneously. Peer-to-peer, uses bandwith appropriately. Other protocols that we can use - espera, udr ...for naming all events and entitites in Reactome - could be applied to any other system37 KB (5,533 words) - 19:17, 11 April 2014
- ...fer bit of file simultaneously. Peer-to-peer, uses bandwith appropriately. Other protocols that we can use - espera, udr ...for naming all events and entitites in Reactome - could be applied to any other system37 KB (5,533 words) - 19:17, 11 April 2014
- ...MC, Biomed Central LTD). During the process of open access image curation, other publishers will be contacted for obtaining copyright permissions. ...the lineage relationship in order to know how images should be handled. In other words, we would like to know which image should be displayed in the express120 KB (19,719 words) - 16:44, 20 October 2023
