GFF Release Data and Changes
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Checking for names in a GFF2 table schema: select distinct fref from fdata where fref like '%Contig2';
Checking for names in a GFF3 table schema: select distinct name from name where name like '%Scaffold122';
WS239
Table name format: genus-initial_species_bioproject-id_release
Example: a_suum_PRJNA62057_WS239
| Table | Data Format | Format Changed from WS238 to WS239? | Landmark Includes Bioproject ID? | |
|---|---|---|---|---|
| a_suum_PRJNA62057_WS239 | GFF3 | no | TBD | |
| a_suum_PRJNA80881_WS239 | GFF3 | no | yes (e.g., As_PRJNA80881_Scaffold122) | |
| b_malayi_PRJNA10729_WS239 | GFF3 | yes | TBD | |
| b_xylophilus_PRJEA64437_WS239 | GFF3 | no | TBD | |
| c_angaria_PRJNA51225_WS239 | GFF3 | no | TBD | |
| c_brenneri_PRJNA20035_WS239 | GFF3 | yes | TBD | |
| c_briggsae_PRJNA10731_WS239 | GFF3 | yes | TBD | |
| c_elegans_PRJNA13758_WS239 | GFF3 | yes | TBD | |
| c_japonica_PRJNA12591_WS239 | GFF3 | yes | TBD | |
| c_remanei_PRJNA53967_WS239 | GFF3 | yes | TBD | |
| c_sp11_PRJNA53597_WS239 | GFF3 | no | TBD | |
| c_sp5_PRJNA194557_WS239 | GFF3 | no | TBD | |
| h_bacteriophora_PRJNA13977_WS239 | GFF3 | no | TBD | |
| h_contortus_PRJEB506_WS239 | GFF3 | no | TBD | |
| l_loa_PRJNA60051_WS239 | GFF3 | no | TBD | |
| m_hapla_PRJNA29083_WS239 | GFF3 | no | TBD | |
| m_incognita_PRJEA28837_WS239 | GFF3 | no | TBD | |
| p_pacificus_PRJNA12644_WS239 | GFF3 | yes | TBD | |
| s_ratti_PRJEA62033_WS239 | GFF3 | no | TBD | |
| t_spiralis_PRJNA12603_WS239 | GFF3 | no | TBD |
GFF3 type and source assignments (via `select * from typelist;`)
Only from C. briggsae right now:
- CDS:WormBase
- CDS:genBlastG
- SL1_acceptor_site:SL1
- SL2_acceptor_site:SL2
- assembly_component:Genbank
- assembly_component:Genomic_canonical
- assembly_component:Link
- complex_substitution:Variation_project
- exon:Transposo
- exon:WormBase
- exon:history
- exon:tRNA_mature_transcript
- expressed_sequence_match:BLAT_Caen_EST_BEST
- expressed_sequence_match:BLAT_Caen_EST_OTHER
- expressed_sequence_match:BLAT_Caen_OST_BEST
- expressed_sequence_match:BLAT_Caen_OST_OTHER
- expressed_sequence_match:BLAT_Caen_RST_BEST
- expressed_sequence_match:BLAT_Caen_RST_OTHER
- expressed_sequence_match:BLAT_Caen_mRNA_BEST
- expressed_sequence_match:BLAT_Caen_mRNA_OTHER
- expressed_sequence_match:BLAT_Caen_ncRNA_BEST
- expressed_sequence_match:BLAT_Caen_ncRNA_OTHER
- expressed_sequence_match:BLAT_Caen_tc1_BEST
- expressed_sequence_match:BLAT_Caen_tc1_OTHER
- expressed_sequence_match:BLAT_EST_BEST
- expressed_sequence_match:BLAT_EST_OTHER
- expressed_sequence_match:BLAT_mRNA_BEST
- expressed_sequence_match:BLAT_mRNA_OTHER
- expressed_sequence_match:EMBL_nematode_cDNAs-BLAT
- expressed_sequence_match:NEMATODE.NET_cDNAs-BLAT
- expressed_sequence_match:NEMBASE_cDNAs-BLAT
- five_prime_UTR:WormBase
- gene:WormBase
- intron:WormBase
- inverted_repeat:inverted
- low_complexity_region:dust
- mRNA:WormBase
- nc_primary_tra
- nc_primary_transcript:history
- nucleotide_match:EXONERATE_BAC_END_BEST
- nucleotide_match:EXONERATE_BAC_END_OTHER
- nucleotide_match:TEC_RED
- primary_transcript:history
- protein_match:UniProt-BLASTX
- protein_match:bmalayi_proteins-BLASTX
- protein_match:cbrenneri_proteins-BLASTX
- protein_match:cbriggsae_proteins-BLASTX
- protein_match:celegans_proteins-BLASTX
- protein_match:cjaponica_proteins-BLASTX
- protein_match:cremanei_proteins-BLASTX
- protein_match:dmelanogaster_proteins-BLASTX
- protein_match:hsapiens_proteins-BLASTX
- protein_match:ppacificus_proteins-BLASTX
- protein_match:scerevisiae_proteins-BLASTX
- pseudogenic_transcript:WormBase
- reagent:Oligo_set
- region:
- repeat_region:
- sequence_motif:translated_feature
- substitution:Allele
- tRNA:tRNA_mature_transcript
- tandem_repeat:tandem
- transcript_region:RNASeq_F_asymmetry
- transcript_region:RNASeq_reads
- transposable_element_CDS:Transposon_CDS
WS238
Table name format: genus-initial_species_bioproject-id_release
Example: a_suum_PRJNA62057_WS238
| Table | Data Format | Format Changed from WS237 to WS238? | Landmark Includes Bioproject ID? | |
|---|---|---|---|---|
| a_suum_PRJNA62057_WS238 | GFF3 | no | no | |
| a_suum_PRJNA80881_WS238 | GFF3 | no | yes (e.g., As_PRJNA80881_Scaffold122) | |
| b_malayi_PRJNA10729_WS238 | GFF2 | no | ? | |
| b_xylophilus_PRJEA64437_WS238 | GFF3 | no | no | |
| c_angaria_PRJNA51225_WS238 | GFF3 | no | no | |
| c_brenneri_PRJNA20035_WS238 | GFF2 | no | ? | |
| c_briggsae_PRJNA10731_WS238 | GFF2 | no | ? | |
| c_elegans_PRJNA13758_WS238 | GFF2 | no | ? | |
| c_japonica_PRJNA12591_WS238 | GFF2 | no | ? | |
| c_remanei_PRJNA53967_WS238 | GFF2 | no | ? | |
| c_sp11_PRJNA53597_WS238 | GFF3 | no | no | |
| c_sp5_PRJNA194557_WS238 | GFF3 | no | no | |
| h_bacteriophora_PRJNA13977_WS238 | GFF3 | no | no | |
| h_contortus_PRJEB506_WS238 | GFF3 | no | no | |
| l_loa_PRJNA60051_WS238 | GFF3 | no | no | |
| m_hapla_PRJNA29083_WS238 | GFF3 | no | no | |
| m_incognita_PRJEA28837_WS238 | GFF3 | no | no | |
| p_pacificus_PRJNA12644_WS238 | GFF2 | no | ? | |
| s_ratti_PRJEA62033_WS238 | GFF3 | no | no | |
| t_spiralis_PRJNA12603_WS238 | GFF3 | no | no |
