Difference between revisions of "WormBase Model:Transcript"
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== Model == | == Model == | ||
<pre> | <pre> | ||
+ | /////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | // ?Transcript class - krb 021126 | ||
+ | // | ||
+ | /////////////////////////////////////////////////////////////////// | ||
+ | ?Transcript Evidence #Evidence | ||
+ | SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transcript | ||
+ | Structure Source_exons Int UNIQUE Int | ||
+ | DB_info DB_remark ?Text #Evidence // was missing from first draft of Transcript class krb | ||
+ | Database ?Database ?Database_field UNIQUE ?Accession_number XREF Transcript | ||
+ | Origin From_laboratory UNIQUE ?Laboratory // [020306 kj] | ||
+ | Species UNIQUE ?Species // [020306 kj] | ||
+ | Visible Gene ?Gene XREF Corresponding_transcript // for live transcripts | ||
+ | Gene_history UNIQUE ?Gene XREF Corresponding_transcript_history // when Transcript is dead | ||
+ | Variation ?Variation XREF Transcript // added to fit two alleles of RNA genes [021127 krb] | ||
+ | Matching_cDNA ?Sequence XREF Matching_transcript #Evidence // to attach non-coding RNA genes to matching ESTs | ||
+ | Corresponding_CDS UNIQUE ?CDS XREF Corresponding_transcript #Evidence // 1-2-1 relationships with coding genes | ||
+ | Corresponding_PCR_product ?PCR_product XREF Overlaps_transcript | ||
+ | Corresponding_oligo_set ?Oligo_set XREF Overlaps_transcript | ||
+ | Reference ?Paper XREF Transcript // [020306 kj] | ||
+ | RNAi_result ?RNAi XREF Transcript //was missing from model [021126 krb] | ||
+ | GO_term ?GO_term XREF Transcript ?GO_code #Evidence // [030411 krb] | ||
+ | Microarray_results ?Microarray_results XREF Transcript //added for Microarray_results | ||
+ | Provisional_description ?Text #Evidence | ||
+ | Detailed_description ?Text #Evidence | ||
+ | Concise_description ?Text #Evidence | ||
+ | Brief_identification UNIQUE Text // [020306 kj] | ||
+ | Confidential_remark ?Text | ||
+ | SAGE_tag ?SAGE_tag XREF Transcript #SAGE_mapping_info | ||
+ | Remark ?Text #Evidence | ||
+ | Properties Transcript UNIQUE mRNA UNIQUE Processed_mRNA | ||
+ | Unprocessed_mRNA | ||
+ | tRNA Type UNIQUE Text // ck1 [030926] krb | ||
+ | Anticodon UNIQUE Text // | ||
+ | rRNA UNIQUE Text | ||
+ | snRNA UNIQUE Text | ||
+ | snoRNA UNIQUE Text // [030102 krb] | ||
+ | scRNA UNIQUE Text | ||
+ | stRNA UNIQUE Text // [010723 dl] | ||
+ | miRNA UNIQUE Text // [020306 kj] | ||
+ | ncRNA UNIQUE Text // true non-coding RNAs | ||
+ | snlRNA UNIQUE Text //small nuclear like | ||
+ | u21RNA UNIQUE Text //21U-RNA | ||
+ | Isoform #Evidence // Set if this is a RNA isoform | ||
+ | Ignore #Evidence // Set for putative NMD targets which we do not want to see in wormrna | ||
+ | Start_not_found // [020306 kj] | ||
+ | End_not_found // [020306 kj] | ||
+ | Associated_feature ?Feature XREF Associated_with_transcript #Evidence | ||
+ | Method UNIQUE ?Method | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == |
Revision as of 15:53, 9 August 2010
Curator Comments/Description
Model
/////////////////////////////////////////////////////////////////// // // ?Transcript class - krb 021126 // /////////////////////////////////////////////////////////////////// ?Transcript Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transcript Structure Source_exons Int UNIQUE Int DB_info DB_remark ?Text #Evidence // was missing from first draft of Transcript class krb Database ?Database ?Database_field UNIQUE ?Accession_number XREF Transcript Origin From_laboratory UNIQUE ?Laboratory // [020306 kj] Species UNIQUE ?Species // [020306 kj] Visible Gene ?Gene XREF Corresponding_transcript // for live transcripts Gene_history UNIQUE ?Gene XREF Corresponding_transcript_history // when Transcript is dead Variation ?Variation XREF Transcript // added to fit two alleles of RNA genes [021127 krb] Matching_cDNA ?Sequence XREF Matching_transcript #Evidence // to attach non-coding RNA genes to matching ESTs Corresponding_CDS UNIQUE ?CDS XREF Corresponding_transcript #Evidence // 1-2-1 relationships with coding genes Corresponding_PCR_product ?PCR_product XREF Overlaps_transcript Corresponding_oligo_set ?Oligo_set XREF Overlaps_transcript Reference ?Paper XREF Transcript // [020306 kj] RNAi_result ?RNAi XREF Transcript //was missing from model [021126 krb] GO_term ?GO_term XREF Transcript ?GO_code #Evidence // [030411 krb] Microarray_results ?Microarray_results XREF Transcript //added for Microarray_results Provisional_description ?Text #Evidence Detailed_description ?Text #Evidence Concise_description ?Text #Evidence Brief_identification UNIQUE Text // [020306 kj] Confidential_remark ?Text SAGE_tag ?SAGE_tag XREF Transcript #SAGE_mapping_info Remark ?Text #Evidence Properties Transcript UNIQUE mRNA UNIQUE Processed_mRNA Unprocessed_mRNA tRNA Type UNIQUE Text // ck1 [030926] krb Anticodon UNIQUE Text // rRNA UNIQUE Text snRNA UNIQUE Text snoRNA UNIQUE Text // [030102 krb] scRNA UNIQUE Text stRNA UNIQUE Text // [010723 dl] miRNA UNIQUE Text // [020306 kj] ncRNA UNIQUE Text // true non-coding RNAs snlRNA UNIQUE Text //small nuclear like u21RNA UNIQUE Text //21U-RNA Isoform #Evidence // Set if this is a RNA isoform Ignore #Evidence // Set for putative NMD targets which we do not want to see in wormrna Start_not_found // [020306 kj] End_not_found // [020306 kj] Associated_feature ?Feature XREF Associated_with_transcript #Evidence Method UNIQUE ?Method