removed underscore from ncRNA_gene for RFAM.

Moved children of regigon to more specific parents.

tracker items 2117006 and 2104189 (flanking_region subtypes and transfrag).

Made some EXACT synonyms within BS BROAD as per 2105691, made children of region (SO:0000001) less confusing as per 2105696 and moved the breakpoints to be children of junction as per 2105705. Also created new breakpoint terms.

Fixed the broken dbxref to out of date websites.

[ 2095595 ] plasmid definition
Updated the definition of the plasmid term to accomodate OBO request.

Updated changed to the structure of the polypeptide_region.
I have moved polypeptide_motif to be a direct child of polypeptide_conserved
region.
Now it is a sib of polypeptide domain.
This makes more sense if you look at the definitions.
Then I added biochemical motif as a synonym of biochemical region, and made it
an is_a child of polypeptide_motif.

I have merged polypeptide_domain with polypeptide_structural_domain.
So polypeptide_domain now has some alt ID’s.
I kept the definition of polypeptide_domain

I moved polypeptide_repeat to be a child of polypeptide_conserved_region

 mature_peptide is_a peptide_region
 Immature_peptide is_a peptide_region
 Cleaved_peptide is_a peptide_region
 mature_protein_region part_of immature_polyp
 cleaved_peptide_region part_of immature_polyp

Fixed persistant warnings about comments.
Removed disjoints from genome.

Moved stop_codon_redefined_* to be children of recoded_codon (SO:0000145) and changed their associated_with relationships to has_part as in tracker item 2075830, and merged kinetoplast_chromosome, maxicircle_chromosome and minicircle_chromosome into kinetoplast, maxicircle and minicircle respectively, as in tracker item 2075800, and changed the maxicircle_gene and minicircle_gene relationships to be part_of.

Definition added for recoded_codon (SO:0000145); see tracker item 2048083.

added cleaved_for_gpi_anchor_region

added defs for nuclease_binding_site (SO:0000059), restriction_enzyme_binding_site (SO:0000061), mRNA_region (SO:0000836), tmRNA_region (SO:0000847) and CDS_region (SO:0000851).

tracker item [ 1917167 ] protein is_a polymer_attribute?
Checking in a single change here as it is a bit strange.
The polymer attribute term 'protein'  was being used incorrectly as a feature
 where the term polypeptide should have been used by a MOD. The two
terms have been merged, and 'polypeptide' has absorbed the SO:0000358 as a
secondary ID, and 'protein' as a synonym.
A new kind of attribute 'peptidyl' has been added to describe proteinaceous
polymers.

Closed out 3 outstanding tracker items.
2038578  incomplete_CDS - added cross product CDS_fragment.
2028033  protein modification regions - added bass types for protein
modification features.
2013408  Definitions of topological features - added definitions to the
attributes circular and linear.

[ 2033019 ] histone binding sites.
Added histone_binding_site as a child of protein_binding_site.
Closed the tracker.

Added more RNA base feature modifications, and updated terms that started with
a number.

Added RNA modification terms.
Fixed white spaces leading and trailing in synonyms.

 2021594 - tracker. Added gene_segment as the base for Alex and Lindsay to
 build the imunnology/recombination terminology.

De-orphaned TATA_box.

Reversed parthood relations for immunological gene clusters and TATA boxes in RNA polymerase regions as per tracker item 1850857.

tracker item 1953535
The Terms for GO annotation of db_object_type
Added 10 kinds of nc_RNA_genes to allow for detailed annotation of the
db_object_type in the GO annotation file.

Tracker items:
1976539 - kinetoplast terms
renamed kinetoplast_sequence, maxicircle-sequence and minicircle_sequence to
kinetoplast, maxicircle and minicircle respectively.
Made maxi and mini kinds of replicon.
defined all 3 terms.
Created sequence_collection.(also for tracker 1911479)
made kinetoplast and genome kinds of sequence collection.
made mini and maxi parts of kinetoplast.

1911479 - bundles
created overlapping_feature_set as a kind of experimental result_region.
created subtype overlapping_EST set, has_part EST.

1978198 - promoter regions and TF_binding sites
moved following to be is_a TF_binding site and part_of RNApol_II_promoter
BRE_motif, CAAT_signal, DPE, e_box, GAGA, INR, MTE and octeamer_motif
moved following to be is_a DNA_motif and part of RNApolII_promoter
DMV1, DMV2, DMV3, DMV4, DMV5, DPE1, NDM2, NDM3, GC_rich_promoter_region
deleted SO:0000844
made c_box part_of RNA_pol_III_promoter_type1, is_a TF_binding_site
deleted SO:0000846
made a_box and b_box part_of RNA_pol_III+promoter_type2, is_a TF_binding_site
deleted SO:0000845
PSE_motif part_of promoter, is_a DNA motif
TATA_box part of RNApol II and III promoters, is_)a TFbs
minus10 and minus 35 signals part of bacterial RNA pol, is_a DNA motif
deleted SO:0000843
removed SO:0000832

Fixed a couple of bad typo's.

Removed the is_symmetric tage from associated_with rel as it was causing the
reasoner to jam.

Fixed typo

Removed the top term (sequence_ontology), renamed operation to be sequence_operation and renamed
replication_mode to be sequence_replication_mode. Also removed the
disjointness between genome, feature mutaton and variation.

Added synonyms to remark.

Added a set of core terms to the working draft directory. (32 terms in total,
using new relationships to describe  the realtions between key terms. One key
thiing is the topological relationships between gene / operon /  and
transcripts make a lot more sense.
Also fixed a couple of typos in so_xp.

created term apicoplast_chromosome - see tracker.

Edited the regulatory regions terms. Removed enhancer part of mRNA, moved
bacterial terminator and moved terminator to part_of transcript.

Fixed hand-edit typo

Added microRNA as synonym as per tracker item 1951465.

Added synonyms to SO:0000003 (G_quartet), SO:0000112 (primer), SO:0000121 (forward_primer), SO:0000132 (reverse_primer) and SO:0000624 (telomere). Tracker ID 1947655.

Added octamer_motif, requested by david Hill and moved SO:0000017 to be a
child of promoter_region as it was in a position too specific for the
definition.

Addressing tracker 1881529
terms with a single subtype.
aneuploid - added synonym polyploid
restriction_enzyme_binding_site - added homing_endonuclease_binding_site
interband - moved to be a sibling of band

fixed typo and updated undefined terms

[ 1894100 ] describing reagents
Renamed vector to be vector_replicon as a child of replicon. A replicon
that has been modified to act as a vector for foreign sequence.

Moved BAC, cosmid, fosmid, lambda_vector, PAC phagemid, YAC and
plasmid_vector to be is_a vector_replicon.

clone is composed of a clone_insert and a replicon_vector
A clone insert may be composed of many cloned_regions

A plasmid_vector derives from a plasmid

DNAzyme moved to be an oligo has_quality enzymic.

enzymic moved to be a feature_attribute

An integrated_plasmid derives_from a plasmid

[ 1889545 ] fragments, fingerprint_contig, maps, has_part
Added physical map based terms to assembly as requested by tracker.
Assembly
    Sequence_assembly :: this used to be called assembly
    fragment_assembly ::aka physical map
       Fingerprint_map
       STS_map
       RH_map

     Assembly_component
       Sonicate_fragment
       Restriction_fragment
         RFLP

New relationships. Tracker items 1917222 and 1911481.
evidence_for_feature
  complete_evidence_for_feature
    partial_evidence_for_feature

Tracker[ 1894100 ] describing reagents
The changes to this tracker item are not yet complete, but this is a start.
EST is_a tag
BAC_end is_a read

New term:
Synthetic_oligo  (needs definition)

GNA_oligo, PNA_oligo, LNA_oligo, NA_oligo and morpholine_oligo are now kinds
of synthetic_oligo

RNAi_reagent is_a ds_oligo

Probe_is_a oligo

Mini_gene is_a ORF *need to remember to add reagent as a quality when I get
that far in the rearrangements.

tracker item 1872208       SO:0001057 enhanceosome - is this really a sequence?
Deleted term.

tracker item [ 1894569 ] miRNA precursor molecule
added pre_miRNA
added miRNA_stem
added miRNA_loop

Updated def of plasmid as Michelle pointed out that not all plasmids are
circular.

tracker item 1903245

tracker_item [ 1904193 ] transcription start site range

Added terms 'base' and 'amino_acid' as per tracker item 1889555. Also renamed processed_transcript and processed_transcript_region to mature_transcript and mature_transcript_region (1903282). Moved aberrant_processed_transcript to be child of transcript.

Added replicon - see tracker item.
Removed plasmid from reagent - made kind of replicon.

Added definitions to antisense, flanked, reverse and forward and mobile_intron.
Made attribute: mobile. Made cross products with mobile intron and MGE.
Deleted intron_attribute.

Renamed illegally-named 7-methylguanine (SO:0001231) to methyl_7_guanine.

Added new terms dihydrouridine, pseudouridine, inosine, 7-methylguanine, ribothymidine and methylinosine as per tracker item 1881912.

Tracker item 1881870 - added four attributes to describe different modes of gene silencing (RNA interference, histone modification, histone methylation and histone deacetylation) and four matching features. Also mentioned relevant GO terms.

Added protein_coding_gene cross product for RB
Added transgeneic_insertion XP for zfin
added retrogene
processed_pseudogene - added synonyms and changed intersection
moved retrotransposed to be a kind of feature attribute, updated definition.
fixed typo in variant_of

Added "homolog", "ortholog" and "paralog" (and UK variants) as EXACT synonyms for "homologous_region" (SO:0000853) and children. Also mended xp of homologous_region.

moved tRNA and archaeal_intron to be sequence_features rather than attributes.
Restructure the kinds of introns. Added endonuclease_spliced_intron, moved
children to be kinds of autocatalytically_spliced_intron. Added definitions.

Updated exon_region subtypes and added missing term for Gabby.

updated the def of snRNA and removed typo from snRNA_primary_transcript.

gabby's changes to the protein terms:

1)
As to disorder I'd be inclined to add it as a direct subclass of
SO:0001070; something like
Name: "Intrinsically unstructured region"
Synonym: "disordered region"
Definition: "A region of polypeptide chain with high conformational
flexibility"

2)
lipoprotein -  a signal for both membrane translocation and lipid
attachment.


*Structural Terms*

4)
alpha_beta_motif
5)
catmat_left_handed_three
6)
catmat_left_handed_four
7)
catmat_right_handed_three
8)
catmat_right_handed_four

*error correction*
The motif name is wrong:
asx_turn_type_right_handed_type_one
should be
asx_turn_right_handed_type_one

Added features to sofa -request by Micheal Han

Tracker items 1874245

+SO:0000345 EST
++ 5_Prime_EST
++3_Prime_EST

and 187415
+ RNA_Polymerase_Promoter
++ Phage_RNA_Polymerase_Promoter
+++ SP6_RNA_Polymerase_Promoter
+++ T3_RNA_Polymerase_Promoter
+++ T7_RNA_Polymerase_Promoter

Corrections to typoes passim. Small corrections to names of SO:0000242 (now untranslated_region_polycistronic_mRNA, "polycistronic" instead of "polyicistronic"), SO:0000848 (now RNApol_II_promoter_region, "RNApol" instead of "RNA") and SO:0001201 (now positive_sense_ssRNA_viral_sequence, "positive" instead of "postive").

Viral terms. After dicussion on song-devel, the viral terms have been update.
The names now reflect that they are viral_sequence, and the definitions are in
line with that.

Added 5 viral terms for John Osborne.

Changed scope for consensus sequences, when used as synonyms, from EXACT to NARROW as per tracker item 1850228. Affects SO:0000015 (DPE_motif), SO:0001157 (DMv4_motif), SO:0001158 (E_box_motif), SO:0001159 (DMv5_motif), SO:0001160 (DMv3_motif), SO:0001161 (DMv2_motif) and SO:0001162 (MTE). Also some tidying of other synonyms.

Updated the definition of exon to be inclusive of the exons of non-coding RNA
transcripts, and to become in line with its position in the ontology. Updated
the definition and position of gene_cassette as per request from SGD.

Added new synthetic nucleic acid types (these are also now present in ChEBI) and their oligos as per tracker item 1850113. Also gave cDNA_clone and genomic_clone the qualities cDNA and genomic_DNA and made cDNA the child of DNA. Added definitions for DNA and RNA.

Renamed single_exon to exon_of_single_exon_gene (SO:0005845), corrected mistake whereby RNase_P_RNA and RNase_MRP_RNA had no parents. See tracker item 1840331.

Started to make polymer_attributes more systematic - SO:0000034 becomes morpholino_oligo, SO:0001011 becomes PNA_oligo, definition for SO:0000358, moved strand_attribute SO:0000983 and direction_attribute SO:0001029 to be feature_attribute, made SO:0000987 and SO:0000988 mutually disjoint; tidied snoRNA terms and cross-productified enzymatic RNA terms as per tracker item 1828882. Exceptions: did not give RNase_P_RNA and RNase_MRP_RNA qualities "enzymatic" as differentia not unique.

Exon tidying - renamed five_ and three_prime_coding_exon_noncoding_region, defined exon_region, defined single_exon with a view to obsoletion, defined interior_exon.

moved gene_cassette and gene_cassette array to be direct is_a chldren of
gene_group.

Added AU_rich_element, iron_responsive_element and Bruno_response_element as per tracker item 1831702. Also fixed typo in internal_Shine_Dalgarno_sequence def.

[ 1828884 ] merge snRNA_4.5S (SO:0005839) into U14_snoRNA (SO:0000403)

Renamed U14_snRNA to U14_snoRNA (SO:0000403), and made into child of C_D_box_snoRNA (SO:0000593) - changed def of snoRNA (SO:0000275) and used old def to make new term U3_snoRNA (SO:0001179) - see tracker item 1827469.

1. made noncoding_exon part of ncRNA
2. Added derives from relationships between ncRNA's and respective primary
transcripts.
--antisense_RNA
--miRNA
--tRNA and 22 children
--snRNA
--SRP_RNA
--snoRNA and 3 children
--scRAN
--rRNA and 2 children

Added systematic sets of synonyms for rRNA and snRNA terms - see tracker item 1827443.

Saved the noncoding_exon change.

Allows SGD to use noncoding_exon

Removed the BS namespace from the ontology. There is a category to identify
these terms.

tracker item 1815741. mergine stem and hairpin

tRNA tracker terms 1815035, 1815029, 1815004.

1814372 and 1814367 Tracker items. Updates to the rRNA terms and a new term rRNA_21S.

Fixed a couple of disapeared terms.

resaved the changes for the virus term.

1811412 - l_s_f.obo saving the correct terms now.

1811364 updated virus terms.

Tracker  1808786  updated the definitions of the pseudogene terms.

I have made the top nodes disjoint from each other.
Tracker request ID 1807279

Tracker id 1799080
Added ds_RNA_virus_sequence

Tracker ID 1806636
TSS is a region not junction.

Moved 4 of the biosapiens terms t more appropriate position.

Added  6 more promoter motifs from the fitzgerald paper.
INR1_motif,
DPE1_motif
DMv1_motif
GAGA_motif
NDM2_motif
NDM3_motif
Renamed the previous terms with _motif to make uniform.

Updating promoter regions.
Added DMv4
E box motif
DMv5
DMv3
DMv2
MTE
as requested by nicole from eth tracker. Please not that I did not use the
names she suggested as these elements had been assigned names in a subsequent
paper (fitzgerald et al)
Also added synomyms to existing terms.

Begining the regulatory motif modifications requested by nicole. Modified
DPE_motif -updated definition, added iupac synonym and new cross ref. Added
DRE_motif.

Fixed tRNA typo list from tracker:[ 1789497 ]

Term tracker [ 1778405 ] beta turn synonyms, definitions and terms. Added the
synonyms and extra beta turn terms as requested by Colin.

tracker 1780344. Added synonyms.

Added new term: polinton SO:0001150

Some of the merged terms from biosapiens retains 2 comments and definitions.
Removed the obo-edit notation, and updated the definiton. Affected terms:
polypeptide_region, sequence_variation_attribute, transit_peptide,
binding_site, mature_peptide_region, polypeptide_domain, and signal peptide.

Tracker requests 17775666 and 1777552 - added synonyms for gamma turns and
schellmann loops.

Update to def of sequence_feature.

Term tracker 1776348 addressed. The definition of sequence_feature included
the word 'region' making it somewhat circular. The definitions of region,
junction and sequence_feature updated.
sequence_feature: An extent of biological sequence.
junction: A sequence_feature with an extent of zero.
region: A sequence_feature with an extent greater than zero.

Added synonyms to G_quartet as requested in term tracker 1774672.

The Biosapiens terms have been merged with SO. These are terms describing
polypeptide features and have been added as children of polypeptide_region,
binding_site, sequence_variation_atribute and remark.
Of the 108 terms in biosapiens, 96 were merged into SO. These terms have SO
UIDs and BS alt_ids. They are also marked with the category biosapiens.
The new terms with ids:
New term:  SO:0000691  "cleaved_initiator_methionine"
New term:  SO:0001061  "propeptide_cleavage_site"
New term:  SO:0001062  "propeptide"
New term:  SO:0001063  "immature_peptide_region"
New term:  SO:0001064  "active_peptide"
New term:  SO:0001066  "compositionally_biased_region"
New term:  SO:0001067  "polypeptide_motif"
New term:  SO:0001068  "polypeptide_repeat"
New term:  SO:0001069  "polypeptide_structural_domain"
New term:  SO:0001070  "structural_region"
New term:  SO:0001071  "membrane_structure"
New term:  SO:0001072  "extramembrane"
New term:  SO:0001073  "cytoplasm_location"
New term:  SO:0001074  "non_cytoplasm_location"
New term:  SO:0001075  "intramembrane"
New term:  SO:0001076  "membrane_loop"
New term:  SO:0001077  "transmembrane"
New term:  SO:0001078  "polypeptide_secondary_structure"
New term:  SO:0001079  "polypeptide_structural_motif"
New term:  SO:0001080  "coiled_coil"
New term:  SO:0001081  "helix_turn_helix"
New term:  SO:0001082  "polypeptide_sequencing_information"
New term:  SO:0001083  "non_adjacent_residues"
New term:  SO:0001084  "non_terminal_residue"
New term:  SO:0001085  "sequence_conflict"
New term:  SO:0001086  "sequence_uncertainty"
New term:  SO:0001087  "cross_link"
New term:  SO:0001088  "disulfide_bond"
New term:  SO:0001089  "post_translational_modification"
New term:  SO:0001090  "covalent_binding_site"
New term:  SO:0001091  "non_covalent_binding_site"
New term:  SO:0001092  "metal_binding"
New term:  SO:0001093  "protein_protein_interaction"
New term:  SO:0001094  "Ca_contact_site"
New term:  SO:0001095  "Co_contact_site"
New term:  SO:0001096  "Cu_contact_site"
New term:  SO:0001097  "Fe_contact_site"
New term:  SO:0001098  "Mg_contact_site"
New term:  SO:0001099  "Mn_contact_site"
New term:  SO:0001100  "Mo_contact_site"
New term:  SO:0001101  "Ni_contact_site"
New term:  SO:0001102  "W_contact_site"
New term:  SO:0001103  "Zn_contact_site"
New term:  SO:0001104  "active_site_residue"
New term:  SO:0001105  "protein_ligand_interaction"
New term:  SO:0001106  "asx_motif"
New term:  SO:0001107  "beta_bulge"
New term:  SO:0001108  "beta_bulge_loop"
New term:  SO:0001109  "beta_bulge_loop_five"
New term:  SO:0001110  "beta_bulge_loop_six"
New term:  SO:0001111  "beta_strand"
New term:  SO:0001112  "antiparallel_beta_strand"
New term:  SO:0001113  "parallel_beta_strand"
New term:  SO:0001114  "helix"
New term:  SO:0001115  "left_handed_helix"
New term:  SO:0001116  "right_handed_helix"
New term:  SO:0001117  "alpha_helix"
New term:  SO:0001118  "pi_helix"
New term:  SO:0001119  "three_ten_helix"
New term:  SO:0001120  "nest"
New term:  SO:0001121  "nest_left_right"
New term:  SO:0001122  "nest_right_left"
New term:  SO:0001123  "schellmann_loop"
New term:  SO:0001124  "schellmann_loop_seven"
New term:  SO:0001125  "schellmann_loop_six"
New term:  SO:0001126  "st_motif"
New term:  SO:0001127  "st_staple"
New term:  SO:0001128  "turn"
New term:  SO:0001129  "asx_turn_left_handed_type_one"
New term:  SO:0001130  "asx_turn_left_handed_type_two"
New term:  SO:0001131  "asx_turn_right_handed_type_two"
New term:  SO:0001132  "asx_turn_type_right_handed_type_one"
New term:  SO:0001133  "beta_turn"
New term:  SO:0001134  "beta_turn_left_handed_type_one"
New term:  SO:0001135  "beta_turn_left_handed_type_two"
New term:  SO:0001136  "beta_turn_right_handed_type_one"
New term:  SO:0001137  "beta_turn_right_handed_type_two"
New term:  SO:0001138  "gamma_turn"
New term:  SO:0001139  "gamma_turn_classic"
New term:  SO:0001140  "gamma_turn_inverse"
New term:  SO:0001141  "st_turn"
New term:  SO:0001142  "st_turn_left_handed_type_one"
New term:  SO:0001143  "st_turn_left_handed_type_two"
New term:  SO:0001144  "st_turn_right_handed_type_one"
New term:  SO:0001145  "st_turn_right_handed_type_two"
New term:  SO:0001146  "sequence_variation_attribute"
New term:  SO:0001147  "natural_variant_site"
New term:  SO:0001148  "mutated_variant_site"
New term:  SO:0001149  "alternate_sequence_site"
New term:  SO:0000419  "mature_peptide" to "mature_protein_region"
New term:  SO:0000912  "asx_turn"

Made changes to the sequence_variation terms as proposed to song_dev list July
25th 2007. These changes include:
New term sequence_alteration - a child of sequence feature which categorizes
the kinds of things that make a sequence different i.e insertions and
deletions. These terms had previously been called sequence_variant. Now the
sequence_variant term, with new ID, hold the terms created at the immunology
workshop: allele etc.

Made changes to regulatory_region.
Subtyped it to give two children transcriptional_cis_regulatory_region and
splicing_regulatory_region.
Rearranged terms under new structure, modified defintions. Aligning with the
regCreative working group.

fixed BAC_cloned_genomic_insert: the differentiae is derives_from BAC

solution to fragmented repeats problem from the term tracker.
Added new relationship "has_part"
Added new terms repeat_fragmant is a repeat, has_quality fragment
transposon_fragment is_a E, has_quality fragment
nested_region is a region
nested_repeat is a nested_region, has_part region, has_part repeat_fragment,
derives_from repeat_region.

member_of is now transitive,
Added/rearranged terms to coordinate with the phigo group - notable change,
added term mobile_genetic_element.
Added definitions for about 40 terms.

Added the term mitron as a kind of miRNA dervied from an intron

Added terms requested by MGED group. forward, reverse, mitochondrial_DNA and
chloroplast_DNA.

Corrected differentia in term predicted_gene

Corrected genus in xp term consensus_mrna

updated the definition of the term gene to A region (or regions) that includes
all of the sequence elements necessary to encode a functional transcript. A
gene may include regulatory regions, transcribed regions and/or other
functional sequence regions.

Made edits from the SO immunology workshop. Added the following terms: allele,
haplotype, genotype, diplotype, genome, polymorphic_sequence_variant. Changed
the name of located_sequence_feature to sequence_feature. Standardised the
format of the mutation terms. Renamed concequences of mutatoin to "mutation".

Added derives_from for Lynn, fixed attenuator typo, moved epitope.

Added epitope, and made chromosome_band a SOFA term.

Removed whitespace in term name

Obsoleted matcch_set.

start and stop codone added to sofa category

added [ 1674983 ] ntr: internal_guide_sequence from tracker

Added wobble base pair - see tracker request # 1667229

Added MNP, intron_domain - see tracker requests 1656390 and 1654344

Added PNA etc

Added low complexity terms and added many more synonyms to the ontology.

Changed some synonyms to be exact rather than related. Fixed a couple of
typos, and line break problems that caused words to run into each other.

Added solo_LTR for Hadi Q and updated SOFA category tags for rRNA terms