Difference between revisions of "WS227 Models.wrm"
From WormBaseWiki
Jump to navigationJump to search| Line 1: | Line 1: | ||
| − | |||
[[WormBase_Models#Model_Change_Summaries |Back]] | [[WormBase_Models#Model_Change_Summaries |Back]] | ||
| Line 12: | Line 11: | ||
| + | Map class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Map | + | ?Map |
| − | Transgene ?Transgene XREF Map | + | Transgene ?Transgene XREF Map |
| − | Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 | + | Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 |
| − | -D XREF Map | + | -D XREF Map |
| + | |||
| + | Gene class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Gene | + | ?Gene |
| − | DB_info Database ?Database ?Database_field ?Accession_number Text //For Darin genbank genpep ids | + | DB_info Database ?Database ?Database_field ?Accession_number Text //For Darin genbank genpep ids |
| − | Human_disease_relevance ?Text #Evidence // Ranjana [110601 pad] | + | Human_disease_relevance ?Text #Evidence // Ranjana [110601 pad] |
| + | |||
| + | Rearrangement class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Rearrangement | + | ?Rearrangement |
| − | Introgression | + | Introgression |
| + | |||
| + | Species class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Species | + | ?Species |
| − | removal of majority of tags with some additions. | + | removal of majority of tags with some additions. |
| + | |||
| + | Sequence class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Sequence | + | ?Sequence |
| − | Checksum | + | Checksum |
| + | |||
| + | Splice Confirmation hash | ||
------------------------------------------- | ------------------------------------------- | ||
| − | #Splice_confirmation | + | #Splice_confirmation |
| − | + | RNASeq ?Analysis Int | |
| − | + | Mass_spec ?Mass_spec_peptide | |
| + | Sequence collection class introduction | ||
------------------------------------------- | ------------------------------------------- | ||
| + | |||
| + | ?Sequence_collection Origin Evidence #Evidence | ||
| + | Name ?Text // name that the author gave this collection | ||
| + | Species UNIQUE ?Species | ||
| + | Strain UNIQUE ?Strain | ||
| + | Laboratory ?Laboratory | ||
| + | Database ?Database ?Database_field ?Accession_number | ||
| + | History First_WS_release Int // first WormBase release this assembly was used | ||
| + | Latest_WS_release Int // latest release where it was used | ||
| + | Supercedes UNIQUE ?Sequence_collection XREF Superceded_by | ||
| + | Superceded_by UNIQUE ?Sequence_collection XREF Supercedes | ||
| + | Remark ?Text | ||
| + | Status UNIQUE Live #Evidence | ||
| + | Suppressed #Evidence | ||
| + | Dead #Evidence | ||
| + | Sequences ?Sequence | ||
| − | + | Homology group class | |
| − | + | ------------------------------------------- | |
| − | |||
| − | |||
| − | ? | + | ?Homology_group |
| − | + | simplification by generating #Homology_type removal of HOPS_group and RIO_group | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | --- | + | #Homology_type KOG |
| + | TWOG | ||
| + | FOG | ||
| + | LSE | ||
| + | NOG //eggNOG - standard cluster | ||
| + | euNOG //eggNOG - eukaryote cluster | ||
| + | meNOG //eggNOG - metazoan cluster | ||
| − | |||
| − | |||
| − | |||
| − | + | Feature class | |
| − | + | ------------------------------------------- | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | + | ?Feature | |
| + | Defined_by_analysis ?Analysis Int | ||
| − | |||
| − | |||
Int addition | Int addition | ||
| + | |||
| + | Transgene class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Transgene | + | ?Transgene |
| + | |||
Significant modifications and cleanup. | Significant modifications and cleanup. | ||
See CVS diff | See CVS diff | ||
| + | |||
| + | Movie class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Movie | + | ?Movie |
| − | -D Transgene ?Transgene XREF Movie | + | -D Transgene ?Transgene XREF Movie |
| + | |||
| + | Gene class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Gene | + | ?Gene |
| − | -D Rescued_by_transgene ?Transgene | + | -D Rescued_by_transgene ?Transgene |
| + | |||
| + | Person class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Person | + | ?Person |
| − | + | Affiliation Text // used for storing institute affiliations that aren't in their Address | |
| + | |||
| + | Address hash | ||
------------------------------------------- | ------------------------------------------- | ||
| − | #Address | + | #Address |
| − | + | Fax Text | |
| + | |||
| + | Molecule class | ||
------------------------------------------- | ------------------------------------------- | ||
| − | ?Molecule | + | ?Molecule |
| − | + | Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad] | |
| − | |||
| − | |||
Latest revision as of 10:00, 26 October 2011
Contents
Models Tagged for WS229
This cycle we see a number of changes/additions to the core models file.
Model Changes
-D denotes removal of tag.
Map class
?Map Transgene ?Transgene XREF Map Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 -D XREF Map
Gene class
?Gene DB_info Database ?Database ?Database_field ?Accession_number Text //For Darin genbank genpep ids Human_disease_relevance ?Text #Evidence // Ranjana [110601 pad]
Rearrangement class
?Rearrangement
Introgression
Species class
?Species removal of majority of tags with some additions.
Sequence class
?Sequence Checksum
Splice Confirmation hash
#Splice_confirmation RNASeq ?Analysis Int Mass_spec ?Mass_spec_peptide
Sequence collection class introduction
?Sequence_collection Origin Evidence #Evidence Name ?Text // name that the author gave this collection Species UNIQUE ?Species Strain UNIQUE ?Strain Laboratory ?Laboratory Database ?Database ?Database_field ?Accession_number History First_WS_release Int // first WormBase release this assembly was used Latest_WS_release Int // latest release where it was used Supercedes UNIQUE ?Sequence_collection XREF Superceded_by Superceded_by UNIQUE ?Sequence_collection XREF Supercedes Remark ?Text Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Sequences ?Sequence
Homology group class
?Homology_group simplification by generating #Homology_type removal of HOPS_group and RIO_group
#Homology_type KOG
TWOG
FOG
LSE
NOG //eggNOG - standard cluster
euNOG //eggNOG - eukaryote cluster
meNOG //eggNOG - metazoan cluster
Feature class
?Feature
Defined_by_analysis ?Analysis Int
Int addition
Transgene class
?Transgene
Significant modifications and cleanup. See CVS diff
Movie class
?Movie -D Transgene ?Transgene XREF Movie
Gene class
?Gene -D Rescued_by_transgene ?Transgene
Person class
?Person
Affiliation Text // used for storing institute affiliations that aren't in their Address
Address hash
#Address
Fax Text
Molecule class
?Molecule
Rearrangement ?Rearrangement ?Phenotype #Evidence //KY [110602 pad]
