Commits for cline

v255_base to v256_preview (2011-08-08 to 2011-08-16) v256

• Updated the swarm timing statistics for Pfam and Scop
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 36, context: html, text, full: html, text
• Renumbered the references so that ref [2] appears in the text before ref [3]
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html - lines changed 9, context: html, text, full: html, text
• Slight change in behavior for downloading antibody 'documents' that are actually split across two or more documents (e.g. the way the HAIB antibody validation has been coming in two distinct files). Assemble the list of files in a slightly cleaner way
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 2, context: html, text, full: html, text
• Modified several tags to adhere to the restriction that tags should be unique.< tag BCLUNGb --- > tag BCLUNG Typo fixed. < description Normal Neonatal Human Microvascular Endothelial Cells (single Donor), Dermal-Derived --- > description Normal Neonatal Human Microvascular Endothelial Cells (single Donnor), Dermal-Derived Documented the relationship between the HEK293 and t-rex cell lines < description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line --- > description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, ATCC number CRL-1573 Added an order URL indicating the Wold lab for something produced in the Wold lab. In such cases, an order URL is less error-prone than a note that it's from the XYZ lab. Nameley, it's less typo prone. < orderUrl http://woldlab.caltech.edu/ Commenting out stanzas that are due to be removed. < #removed per Redmine #222 < #term UW-5C-Myc-Region < #tag UW5CMYC < #type region < #description Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929) < < #term UW-5C-Gene-Regions < #tag UW5CGENE < #type region < #description Set of 25 regions interrogated in UW 5C gene-targeted experiments --- > term UW-5C-Myc-Region > tag UW5CMYC > type region > description Myc upstream gene desert region used in UW 5C experiments (hg19 chr8:126445818-130737929) > term UW-5C-Gene-Regions > tag UW5CGENE > type region > description Set of 25 regions interrogated in UW 5C gene-targeted experiments A significantly-improved comment < description Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). > description Contigs Commenting out a deprecated stanza < #FastQ is now deprecated < #term Fastq < #tag FASTQ < #type view < #label Fastq < #description Raw sequence with Phred33 quality scores > term Fastq > tag FASTQ > type view > label Fastq > description Raw sequence with Phred33 quality scores A much better description for a new stanza < label Genes De Novo < description 'De novo' genes defined by Cufflinks with FPKM. --- > label Genes DeNovo > description Expression estimates for genes defined by Cufflinks in de novo mode in gtf format Another much better description < description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions --- > description TopHat-defined splice junctions New stanzas < term PeakSeqConservPeaks < tag PSCPEAKS < type view < label PeakSeq Conserved Peaks < description Regions of conserved enriched signal in experiment performed by PeakSeq < < term PeakSeqOptimalPeak < tag PSOPEAKS < type view < label PeakSeq Optimal Peaks < description Regions of optimal enriched signal in experiment performed by PeakSeq < < #snippet for UW5c's primer view < term Primer < tag Primer < type view < label Primer < description placeholder for Uw5c's primer file, so it can be in metaDb properly < < term SppConservPeaks < tag SCPPEAKS < type view < label Spp Conservative Peaks < description Regions of optimal enriched signal in experiment performed by Spp < < term SppOptimalPeaks < tag SOPPEAKS < type view < label SPP Optimal Peaks < description Regions of conserved enriched signal in experiment performed by SPP < Another improved description < description 'De novo' transcripts with FPKM produced by Cufflinks --- > description Transcript models and expression estimates in FPKM produced by Cufflinks in de novo mode Another new stanza < term UniformSignal < tag UNISIG < type view < label Uniform Signal by AWG < description Uniform Signal < Other cases of tags renamed to make all tags will be unique. < tag CNVdt --- > tag CNV < tag SANGER --- > tag GENCODE < tag LICRm --- > tag LICR < tag CALTECHm --- > tag CALTECH < tag UMASSm --- > tag UMASS < tag DUKEm --- > tag DUKE < tag PSUm --- > tag PSU < tag UWm --- > tag UW < tag STANFORDm --- > tag STANFORD < tag YALEm --- > tag YALE < tag CONTROLi --- > tag CONTROL Change in case < validate none > validate None Unclear why this was added... < labInst California Institute of Technology 9523d9481 < label Carninci - RIKEN Omics Science Center 9658c9616
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 516, context: html, text, full: html, text
• Various tags were changed slightly to make all tags unique. This comment wasremoved when the tags were changed, as it's no longer accurate < #same tag as BC_Lung_H12817N Tags now unique < tag BCLUNG --- > tag BCLUNGb The BJ cell line issue. It looks like except for the main cell line, all the others are commented out (deprecated? set aside for now?). < protocol Stam:BJ_Stam_protocol.pdf --- > #protocol Stam:BJ-tert_Stam_protocol.pdf > # JEFF: Please read and find which of these protocols is correct for BJ and label it appropriately > > #These terms seem to have a lot of confusion and no one is currently using these cell lines. We are commenting out until resovled see Bug#4536 > #term BJ-5ta > #tag BJ5TA > #type Cell Line > #organism human > #description BJ foreskin fibroblast transfected with the pGRN145 hTERT, expressing T antigens of SV40 virus.(PMID: 9916802) > #tissue Skin > #vendorName ATCC > #vendorId CRL-4001 > #orderUrl http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-4001&Template=cellBiology > #karyotype normal > #termId BTO:0001255 > #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255 > #sex M > #tier 3 > #protocol Struhl:BJ_5ta_Struhl_protocol.pdf > # > #term BJ-HRas > #tag BJHRAS > #type Cell Line > #organism human > #description hTERT/BJ skin fibroblasts expressing T antigens of SV40 virus and H-RasV12 > #tissue Skin > #vendorName Struhl laboratory > #vendorId BJ-HRas > #orderUrl https://struhl.med.harvard.edu/ > #karyotype normal > #termId BTO:0001255 > #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255 > #sex M > #tier 3 > #protocol Struhl:BJ-tert-HRas_Struhl_protocol.pdf > # > # > #term BJ-T > #tag BJT > #type Cell Line > #organism human > #description foreskin fibroblast > #tissue Skin > #vendorName Struhl laboratory > #vendorId BJ-T > #orderUrl https://struhl.med.harvard.edu/ > #karyotype normal > #termId BTO:0001255 > #termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0001255 > #sex M > #tier 3 > #protocol Struhl:BJ-5ta_Struhl_protocol.pdf New cell line - with issues, the vendorId should not be [1]. This comes from taking the output of the wiki scraping script literally... < term Colo829 < tag COLO829 < type Cell Line < tier 3 < organism human < description Malignant Melanoma < lineage missing < karyotype missing < sex M < tissue Skin < vendorName < vendorId [1] < orderUrl http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1974&Template=cellBiology < lab Crawford < protocol Crawford:Colo829_Crawford_protocol.pdf < More new cell lines. This one looks fine. < term GM12866 < tag GM12866 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex M < tissue Blood < vendorName Coriell < vendorId GM12866 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12866&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12866_Stam_protocol.pdf < This one looks fine too < term GM12867 < tag GM12867 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex F < tissue Blood < vendorName Coriell < vendorId GM12867 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12867&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12867_Stam_protocol.pdf < This one looks fine < term GM12868 < tag GM12868 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex F < tissue Blood < vendorName Coriell < vendorId GM12868 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12868&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12868_Stam_protocol.pdf < Looks fine < term GM12869 < tag GM12869 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex F < tissue Blood < vendorName Coriell < vendorId GM12869 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12869&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12869_Stam_protocol.pdf < Fine < term GM12870 < tag GM12870 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex M < tissue Blood < vendorName Coriell < vendorId GM12870 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12870&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12870_Stam_protocol.pdf < Fine < term GM12871 < tag GM12871 < type Cell Line < tier 3 < organism human < description B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment: Epstein-Barr Virus transformed. < lineage mesoderm < karyotype missing < sex M < tissue Blood < vendorName Coriell < vendorId GM12871 < orderUrl http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM12871&PgId=166 < termId BTO:0002062 (non-specific) < termUrl http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=BTO&termId=BTO%3A0002062&termName=B-lymphoblastoid%20cell%20line < lab Stam < protocol Stam:GM12871_Stam_protocol.pdf < Another new cell line, with vendor ID issues < term Ishikawa < tag ISHIKAWA < type Cell Line < tier 3 < organism human < description endometrial adenocarcinoma < lineage missing < karyotype missing < sex F < tissue Uterus < vendorName < vendorId [3] < orderUrl http://www.sigmaaldrich.com/catalog/ProductDetail.do?D7=0&N5=SEARCH_CONCAT_PNO%7CBRAND_KEY&N4=99040201%7CSIGMA&N25=0&QS=ON&F=SPEC < lab Crawford < protocol Crawford:Ishikawa_Crawford_protocol.pdf < An improved comment had been marked as provisional < description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line (PROVISIONAL) --- > description Human embryonic kidney cells transformed with Adenovirus 5 DNA stably expressing tetracycline repressor, HEK293 (ATCC number CRL-1573) is the parental cell line Lot numbers added < lab Snyder, Myers < lots I1010 (Myers) --- > lab Snyder A new antibody, with issues. The validation type should be in the validation document label, in place of the word "missing". < term CEBPD_(SC-636) < tag CEBPDSC636 < type Antibody < antibodyDescription Rabbit polyclonal IgG, epitope mapping at the C-terminus of CEBPD of human origin. < target CEBPD < targetDescription The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions. It can also form heterodimers with the related protein CEBP-alpha. The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages. The cytogenetic location of this locus has been reported as both 8p11 and 8q11 (provided by RefSeq). < vendorName Santa Cruz Biotech < vendorId sc-636 < orderUrl http://www.scbt.com/datasheet-636-c-ebp-delta-m-17-antibody.html < lab Myers < lots C1010 < targetId GeneCard:CEBPD < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=CEBPD < validation CEBPD_(SC-636)(missing):human_CEBPD_SC-636_validation_Myers.pdf < < A new validation document (with issues, that "missing" shouldn't be there, and the validation type should be there instead) < validation ELK4(missing):human_ELK4_validation_Farnham.pdf --- > validation missing New antibody. This one doesn't have a validation document yet, and shouldn't be registered without one. < term FOSL1_(sc-605) < tag FOSL1SC605 < type Antibody < antibodyDescription Rabbit polyclonal antibody raised against the N-terminus of FOSL1 of rat origin. < target FOSL1 < targetDescription The Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. (provided by RefSeq) < vendorName Santa Cruz Biotech < vendorId sc-605 < orderUrl http://www.scbt.com/datasheet-605-fra-1-r-20-antibody.html < lab Wold < lots G0109 < targetId Genecard:FOSL1 < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=FOSL1 < validation missing New antibody, looks fine except for the missing validation document 5620,5636d5500 < term H3ac_(06-599) < tag H3AC06599 < type Antibody < antibodyDescription rabbit polyclonal antibody raised against a KLH-conjugated p < eptide corresponding to amino acids 1-20 of Tetrahymena histone H3 (ARTKQTAR[K*] < STGG[K*]APRKQLC) where K* is acetylated < target H3ac < targetDescription missing < vendorName Millipore < vendorId 06-599 < orderUrl http://www.millipore.com/catalogue/item/06-599 < lab Wold < lots missing < targetId Genecard:HIST2H3C < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C < validation missing < Another new antibody, missing validation doc < term H3K4me2_(ab32356) < tag H3K4ME2AB32356 < type Antibody < antibodyDescription Rabbit polyclonal < target H3K4me2 < targetDescription Histone H3 (di methyl K4). Marks promoters and enhancers. < vendorName Abcam < vendorId ab32356 < orderUrl http://www.abcam.com/Histone-H3-di-methyl-K4-antibody-Y47-ChIP-Grade-ab32356.html < lab Wold < lots 870402 < targetId Genecard:HIST2H3C < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C < validation missing < Another missing validation < term H3K79me2_(ab3594) < tag H3K79ME2AB3594 < type Antibody < antibodyDescription Rabbit polyclonal < target H3K79me2 < targetDescription H3K79me2 is a mark of the transcriptional transition region - the region between the initiation marks (K4me3, etc) and the elongation marks (K36me3) < vendorName Abcam < vendorId ab3594 < orderUrl http://www.abcam.com/Histone-H3-di-methyl-K79-antibody-ChIP-Grade-ab3594.html < lab Wold < lots 836403 < targetId Genecard:HIST2H3C < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C < validation missing < Same < term H3K79me3_(ab2621) < tag H3K79ME3AB2621 < type Antibody < antibodyDescription Rabbit polyclonal < target H3K79me3 < targetDescription Associated with the gene body of actively transcribed genes < vendorName Abcam < vendorId ab2621 < orderUrl http://www.abcam.com/Histone-H3-tri-methyl-K79-antibody-ChIP-Grade-ab26 < 21.html < lab Wold < lots 805949 < targetId Genecard:HIST2H3C < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=HIST2H3C < validation missing < And another. I don't understand why this one is registered without its validation document. < term MyoD_(sc-32758) < tag MYODSC32758 < type Antibody < antibodyDescription mouse monoclonal antibody raised against recombinant MyoD of < mouse origin with an epitope mapping to amino acids 180-189 < target MyoD < targetDescription This gene encodes a nuclear protein that belongs to the basic < helix-loop-helix family of transcription factors and the myogenic factors subfam < ily. It regulates muscle cell differentiation by inducing cell cycle arrest, a p < rerequisite for myogenic initiation. The protein is also involved in muscle rege < neration. It activates its own transcription which may stabilize commitment to m < yogenesis. (provided by RefSeq) < vendorName Santa Cruz Biotech < vendorId sc-32758 < orderUrl http://www.scbt.com/datasheet-32758-myod-5-8a-antibody.html < lab Wold < lots missing < targetId Genecard:MyoD1 < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=MyoD1 < validation missing < Same < term Myogenin_(sc-12732) < tag MYOGENINSC12732 < type Antibody < antibodyDescription mouse monoclonal antibody; epitope mapping within amino acid < s 138-158 of myogenin of rat origin < target Myogenin < targetDescription Myogenin is a muscle-specific transcription factor that can in < duce myogenesis in a variety of cell types in tissue culture. It is a member of < a large family of proteins related by sequence homology, the helix-loop-helix (H < LH) proteins. It is essential for the development of functional skeletal muscle. < (provided by RefSeq) < vendorName Santa Cruz Biotech < vendorId sc-12732 < orderUrl http://www.scbt.com/datasheet-12732-myogenin-f5d-antibody.html < lab Wold < lots missing < targetId Genecard:Myog < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=Myog < validation missing < < term MEF2_(sc-17785) < tag MEF2SC17785 < type Antibody < antibodyDescription mouse monoclonal antibody raised against amino acids 1-300 m < apping at the N-terminus of MEF-2A of human origin; recommended for detection of < a broad range of MEF-2 family members of mouse, rat and human origin < target MEF2 < targetDescription The MADS box transcription enhancer factor 2 (MEF2) family of < proteins plays a role in myogenesis. < vendorName Santa Cruz Biotech < vendorId sc-17785 < orderUrl http://www.scbt.com/datasheet-17785-mef-2-b-4-antibody.htmllab Wold < lots missing < targetId Genecard:MEF2A < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=MEF2A < validation missing < A new validation document < validation SETDB1(missing):human_SETDB1_validation_Farnham.pdf --- > validation missing This new antibody looks fine, yay! < term ZNF274_(M01) < tag ZNF274M01 < type Antibody < antibodyDescription Mouse monoclonal antibody raised against a partial recombinant ZNF274 (corresponding to amino acids 420-531 of the human ZNF274 protein).target ZNF274targetDescription ZNF274 is a zinc finger protein containing five C2H2-type zinc finger domains, two Kruppel-associated box A (KRABA) domains, and a leucine-rich SCAN domain. The encoded protein has been suggested to be a transcriptional repressor and interacts with the KAP1 corepressor complex. < vendorName Abnova ZNF74 < vendorId M01 < orderUrl http://www.abnova.com/products/products_detail.asp?Catalog_id=H00010782 < -M01 < lab Farnham < lots 08064-4C12 < targetId GeneCards:Genecard:ZNF274 < targetUrl http://www.genecards.org/cgi-bin/carddisp.pl?gene=Genecard:ZNF274 < validation ZNF274_(M01)(missing):human_ZNF274_M01_validation_Farnham.pdf < Several new views. < term Control_32bp < tag CNTRL32B < type control < description This data represents a control being compared to experiments using read length of 32 bp PROVISIONAL < < term Control_36bp < tag CNTRL36B < type control < description This data represents a control being compared to experiments using read length of 36 bp PROVISIONAL < < term Control_50bp < tag CNTRL50B < type control < description This data represents a control being compared to experiments using read length of 50 bp PROVISIONAL < (unsure) > term DIFF_7d > tag DIFF7D > description Grown for 7 days in differentiation medium (Wold) > type treatment > Several new treatments < term Myoblast < tag MYB < description Grown differentiation medium undifferediated (Wold) PROVISIONAL < type treatment < < term Myocyte_24h < tag MYC24H < description Grown for 24 hours in differentiation medium (Wold) PROVISIONAL < type treatment < < term Myocyte_60h < tag MYC60H < description Grown for 60 hours in differentiation medium (Wold) PROVISIONAL < type treatment < < term Myocyte_5d < tag MYC5D < description Grown for 5 days in differentiation medium (Wold) PROVISIONAL < type treatment < < term Myocyte_7d < tag MYC7D < description Grown for 7 days in differentiation medium (Wold) PROVISIONAL < type treatment < < < < Several improved descriptions < description PROVISIONAL Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). --- > description Contigs represent continuous regions of the genome that are covered by several overlapping RNA-seq reads. The score represents the logarithm of the expression level (read coverage depth). 8741c8449 < description 'De novo' genes defined by Cufflinks with FPKM. PROVISIONAL --- > description 'De novo' genes defined by Cufflinks with FPKM. 8777c8485 < description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions PROVISIONAL --- > description TopHat-defined (Caltech) or STAR-defined (CSHL) splice junctions 8802c8510 < description Regions of conserved enriched signal in experiment performed by PeakSeq (PROVISIONAL) --- > description Regions of conserved enriched signal in experiment performed by PeakSeq 8808c8516 < description Regions of optimal enriched signal in experiment performed by PeakSeq (PROVISIONAL) --- > description Regions of optimal enriched signal in experiment performed by PeakSeq 8929c8637 < description Regions of optimal enriched signal in experiment performed by Spp (PROVISIONAL) --- > description Regions of optimal enriched signal in experiment performed by Spp 8935c8643 < description Regions of conserved enriched signal in experiment performed by SPP (PROVISIONAL) --- > description Regions of conserved enriched signal in experiment performed by SPP 8977c8685 < description Uniform Signal (PROVISIONAL) --- > description Uniform Signal Tag modified to make it unique < tag CNV --- > tag CNVdt New status stanzas < ## object Status < term revoked < tag REVOKED < type objStatus < description This file has been REVOKED by the submitting laboratory for some reason. It should not be used for further research. PROVISIONAL < < term replaced < tag REPLACED < type objStatus < description This file has been REPLACED by the submitting laboratory with an improved version. PROVISIONAL < Several tags modified to make them unique. < tag GENCODE --- > tag SANGER 9961c9658 < tag LICR --- > tag LICRm 9972c9669 < tag CALTECH --- > tag CALTECHm 9983c9680 < tag UMASS --- > tag UMASSm 9994c9691 < tag DUKE --- > tag DUKEm 10005c9702 < tag PSU --- > tag PSUm 10017c9714 < tag UW --- > tag UWm 10028c9725 < tag STANFORD --- > tag STANFORDm 10039c9736 < tag YALE --- > tag YALEm 10278d9974 < hidden yes Various priorities modified by Cricket < priority 590 --- > priority 500 10333c10029 < priority 415 --- > priority 500 10342d10037 < hidden yes 10344c10039 < priority 470 --- > priority 991 10354c10049 < priority 110 --- > priority 120 More tags modified to make them unique < tag CONTROL --- > tag CONTROLi More priorities modified by Cricket < priority 325 --- > priority 235 10519c10214 < priority 590 --- > priority 500 10533c10228 < priority 590 --- > priority 500 10574c10269 < priority 166 --- > priority 500 10625c10320 < priority 590 --- > priority 500 10635c10330 < priority 150 --- > priority 160 10645c10340 < priority 430 --- > priority 500 10656,10667c10351 < priority 999 < New stanza < term objStatus < tag OBJSTAT < type typeOfTerm < label Object Status < description The status of the file or table object (revoked, replaced, etc) PROVISIONAL < searchable no < hidden no < cvDefined yes < validate cv < priority 1 --- > priority 500 More new priorities. < priority 242 --- > priority 460 10753c10437 < priority 165 --- > priority 500 10794c10478 < priority 160 --- > priority 150 10814c10498 < priority 430 --- > priority 500 10875c10559 < priority 430 --- > priority 921 10885c10569 < priority 120 --- > priority 110 10959c10643 < priority 590 --- > priority 500
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 475, context: html, text, full: html, text
• Changing the makefiles to move a bit closer to Venkat's new makefile specification. I still need to get the rest of the specification details from Venkat
  • src/hg/encode/antibodyWikiParser/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser/makefile - lines changed 4, context: html, text, full: html, text
• Added appropriate text to the ENCODE Proteogenomics supertrack page
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html - lines changed 72, context: html, text, full: html, text
• Fixed an incorrect page title
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html - lines changed 1, context: html, text, full: html, text
• Added the UNC/BSU ProtGeno track to the new ProtGeno supertrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 1, context: html, text, full: html, text
• Cleaned up the usage for both wiki scraping scripts
  • src/hg/encode/antibodyWikiParser/antibodyWikiParser.py - lines changed 28, context: html, text, full: html, text
  • src/hg/encode/cellTypeParser/cellTypeParser.py - lines changed 29, context: html, text, full: html, text
• Added a protocol SDS-Page declaration for the current data, so that when the FASP data is added, it will be easier and clearer to integrate
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeUncBsuProt.ra - lines changed 12, context: html, text, full: html, text
• Added two proteogenomics protocols
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 11, context: html, text, full: html, text