changes.txt

Dec 20, 2024
  DO synonym loader: updated to resolve obsolete terms

Nov 15, 2024
  GO taxon constrains: added handling of obsolete terms

Nov 12, 2024
  EfoXrefGenerator: fixed -- created synonyms should always have type set to 'xref'

Oct 28, 2024
  CL ontology: updated to release v2024-09-26

Aug 09, 2024
  loader: added security check to prevent processing (loading) of ontologies developed and maintained in RGD
          (CMO, MMO, XCO, PW, RS and RDO)

Aug 08, 2024
  SSSOMGenerator: added generation of RDO to MIM file

Jul 29, 2024
  added EfoXrefGenerator to generate reciprocal EFO xrefs for VT, MP, HP, CMP and RDO ontologies

Jul 25, 2024
  added SSOM TSV file validator
  draft version of SSSOM file generator

Jul 16, 2024
  CL ontology: updated to release v2024-07-10

Jul 08, 2024
  CL ontology: updated to release v2024-05-15
  CL ontology: improved loading of 'develops-from' relations

Jun 17, 2024
  patch to remove cyclic GO CC relationships

May 15, 2024
  TermStatsLoader: updating to include rgdvariant type for GWAS variant annotations

May 14, 2024
  OboFileCreator: 'primary_id' synonyms are exported as 'xref', not ad 'alt_id'
    also malformed accessions in 'xref' and 'alt_id' fields are no longer exported

Apr 11, 2024
  CL ontology: updated to release v2024-04-05

Feb 13, 2024
  CL ontology: updated to release v2024-02-13

Feb 12, 2024
  TaxonConstraints loader: added qc to ensure GO terms are in RGD db
  cleanup: removed unused 'gviewer_stats' logger

Jan 08, 2024
  updated CL source to CL release 2024-01-04

Dec 08, 2023
  updated CL source

Dec 04, 2023
  implemented EfoXrefCreator: to create xrefs for EFO ontology
    based on xrefs in other ontologies referencing EFO

Nov 28, 2023
  better mapper for EFO-VT
  new source for VT ontology

Nov 07, 2023
  EFO-CMO loader

Oct 30, 2023
  better parsing for EFO ontology

Oct 23, 2023
  updated CL source to CL release 2023-10-19

Oct 04, 2023
  updated CL source to CL release 2023-09-21

Sep 25, 2023
  removed obsolete code to precompute gviewer data in ONT_TERM_STATS table

Aug 25, 2023
  updated CL source to CL release 2023-08-24

Jul 24, 2023
  updated CL source to CL release 2023-07-20
  EfoLoader: limits input to GWAS records having a single EFO entry
  parser: ignoring lines 'property_value: term_tracker_item ...'
  parser: loading lines 'property_value: IAO:0000028 ...' as synonyms

Jul 05, 2023
  obo validator script: added generation of ofn file (owl functional) in addition to owl file

Jun 23, 2023
  updated CL source to CL release 2023-06-22

May 30, 2023
  OboFileCreator: changed the way dbxrefs in definitions are generated

May 23, 2023
  updated CL source to CL release v2023-05-22

May 22, 2023
  removed from scripts calls to GViewerStatsLoader -- this loader is obsolete and table ONT_TERM_STATS it populates
    is not being used anymore (for quite awhile, already)

May 03, 2023
  implemented FileSystemLock in TermStatsLoader: only one instance of TermStatsLoader could be running in a JVM
  TermStatsLoader: stats computation executes in parallel using no more than specified nr of threads

Apr 25, 2023
  updated CL source to CL release v2023-04-20

Apr 21, 2023
  EfoBulkLoad updated to load HP/MP mappings

Apr 11, 2023
  updated CL source to CL release v2023-03-21
  enhanced parsing of date fields

Apr 06, 2023
  better EFO ontology loading for EFO:BAO terms

Apr 05, 2023
  fixed EFO ontology loading -- was spuriously adding 'EFO:GO:xxxxxxx' terms with 'BP','CC','MF' ont_id

Apr 04, 2023
  fixed generate_obo_file.sh

Mar 17, 2023
  further improvements in loading EFO ontology

Mar 10, 2023
  EFO xrefs loading tune up

Mar 09, 2023
  implemented loading of EFO ontology -- first attempt

Mar 06, 2023
  updated EfoMapper to limit EFO terms to EFO terms appearing in GWAS data

Mar 02, 2023
  updated EfoBulkLoad to also load synonyms

Feb 17, 2023
  updated build.gradle to be gradle 6.x + compatible
  updated CL source to CL release v2023-02-15
  DoQC: optimized code

Jan 20, 2023
  updated source for CL ontology
  removed unused jar dependency
  suppressed dag deletion for malformed obo files

Nov 01, 2022
  DO-QC: added extensive qc of MESH ids

Oct 25, 2022
  EfoBulkLoad: allows to bulk load EFO/MONDO synonyms from a file

Oct 05, 2022
  OmimPsCustomDoTermMapper: tune up (to handle situation where one OMIM:PS is associated with multiple RDO terms)

Aug 26, 2022
  parser: tuned up logging

Aug 01, 2022
  parser: better handling of MESH ids
  EFO-to-RDO mapper: finished EFO-to-MP and EFO-to-HP mappers

Jul 26, 2022
  fix to prevent erroneous deletion of dags / obsoletion of terms
  MP ontology: added loading of ORCID ids into 'created_by' field
  EFO-to-RDO mapper: refactored code to allow adding EFO-to-MP and EFO-to-HP mappers in the future

Jul 22, 2022
  added EFO-to-RDO mapper

Jun 21, 2022
  TaxonConstraints: fixed a bug preventing proper generation and cleanup of Not4Curation synonyms for GO terms

Jun 06, 2022
  DO qc: updated loading of term definitions

Mar 25, 2022
  go constraints: tuned up logging

Mar 24, 2022
  updated rat lineage (NCBI taxonomy)
  go constraints: switched to new source files (old source files no longer available)

Mar 17, 2022
  deployed OmimPsCustomDoTermMapper, to populate table OMIM_PS_CUSTOM_DO

Mar 08, 2022
  do qc: implemented checking of OMIM:PS ids (if they are assigned to the same terms in RGD as they are in DO)

Feb 14, 2022
  parser: updated to allow loading of MONDO ontology

Feb 10, 2022
  DO qc: fixed handling of UTF-8 characters

Jan 04, 2022
  obo exporter: config fix (was using retired ftp://ftp.rgd.mcw.edu)

Dec 20, 2021
  parser: UBERON ontology: 'mutually_spacially_disjoint_with' relationship loaded as synonyms to avoid cycles
  upgraded log4j to avoid zero day vulnerability

Sep 14, 2021
  refactor loader to simplify code and use java streams

Jul 26, 2021
  parser: treats all files as UTF-8-encoded
    (previously most files were considered ISO-8859-1 encoded, and some UTF-8 encoded;
     that resulted in garbled characters being loaded, because now everybody is using UTF-8 encoding)

Jul 21, 2021
  loader: added removal of cyclic relationship for UBERON

Jun 18, 2021
  TermStatsLoaderWithFilter: fixed handling of species list (verver, molerat were missing)

Apr 29, 2021
  tuned up OBO validation script

Feb 4, 2021
  fixed OBO validation script

Jan 27, 2021
  CL,MI,SO,UBERON ontologies: updated sources (files for these ontologies did not change for 9+ months)
  security: the value of api key is now stored in an external property file api.key (not in the code)

Jan 13, 2021
  obo exporter fix: added escaping of double quote characters in term definitions
  DO loader: fixed loading of definition dbxrefs
  scripts: added script to validate OBO files against OBO spec

Dec 22, 2020
  DO QC: improved handling of xref synonyms

Aug 10, 2020
  fixed script run_stats_update_only.sh

Jul 24, 2020
  DO QC loader: better code to load definition xrefs

Jul 06, 2020
  gviewer stats: simplified code; only processing ontologies without cycles

Jul 03, 2020
  obo file creator: updated code to export term def xrefs

Jul 02, 2020
  parser: updated code to load term def xrefs

Jun 08, 2020
  obo generator: improved summary email

Apr 24, 2020
  term stats loader with filter: added calculation of term stats for cell lines

Apr 23, 2020
  term stats loader: added calculation of term stats for cell lines

Apr 15, 2020
  parser: for GO, fixed generation of Not4Curation synonyms

Apr 07, 2020
  obo-generator: vastly improved summary email

Mar 16, 2020
  gviewer stats loader: fix due to changes in rgdcore regarding primaray ref assemblies

Mar 06, 2020
  DO loader: added parsing of broad synonyms

Feb 28, 2020
  DO loader: added QC of OMIM IDs that are in DO ontology but not present in RDO

Dec 04, 2019
  added code to load CVCL ontology (cellosaurus ontology)
  removed code for unused cmdline option '-drop_synonyms'
  DO ontology: added loading of 'ICD9:' and 'ICD10:' xrefs

Nov 25, 2019
  code tune-up to load EFO ontology

Oct 18, 2019
  obo-generator: added export of subsets

Sep 30, 2019
  term stats loader: simplified code

Sep 20, 2019
  added script check_for_cycles.sh

Jul 1, 2019
  loader: fixed loading of term comments
    if a term comment contains new line, carriage return or tab character(s), they are replaced by a space character
    otherwise, we could get Oracle CHECK violation exception

Jun 19, 2019
  DO ontology: added loading of 'NCI:' and 'ICD-O' xrefs

Jun 10, 2019
  updated URL for MP ontology (to use MGI FTP url, instead of http://ontologies.berkeleybop.org)
  -- MGI said that they will be phasing out commits of MP ontology to berkeleybop.org

May 17, 2019  v.1.5.55
  updated URL for GO ontology (to use daily snapshots instead of monthly)

May 01, 2019  v.1.5.54
  DoLoader: added reporting of obsolete OMIM ids present in DO file

Apr 04, 2019  v.1.5.53
  HPO root term name is overridden to be 'Human phenotype' -- the original root term name, which was 'All',
    will become the root term synonym
  fixed issue of orphaned GO terms that should have been obsoleted by the pipeline

Feb 11, 2019  v.1.5.52
  updated source url for GO.obo file

Jan 15, 2019  v.1.5.51
  fixed generation of OBO files with synonyms having synonymtypedefs

Sep 28, 2018  v.1.5.50
  moved from subversion to github

Aug 20, 2018  v.1.5.49
  OboFileGenerator: fix to skip exporting xrefs without value (to avoid NullPointerException)

Aug 20, 2018  v.1.5.49
  OboFileGenerator: fix to skip exporting xrefs without value (to avoid NullPointerException)

Jul 11, 2018  v.1.5.47
  OboFileGenerator: properly emits synonymtypedef DISPLAY_SYNONYM

Jun 12, 2018  v.1.5.46
  TermStatGenerator: fixed issue with 'child_term_count' and 'parent_term_count'

Jun 4, 2018  v.1.5.45
  OboFileGenerator: fixed potential date conversion issue when running in multi-thread environment

May 31, 2018  v.1.5.44
  RDO ontology can be exported to FTP site

May 30, 2018  v.1.5.43
  PW,CMO,MMO and XCO ontologies can be exported to FTP site (logic and script fixes)

May 29, 2018  v.1.5.42
  Term xrefs are no longer loaded into ONT_XREFs table -- they are loaded as synonyms with type 'xref' instead

May 25, 2018  v.1.5.41
  PW,CMO,MMO and XCO ontologies can be exported to FTP site

Apr 30, 2018  v.1.5.40
  removed CMO,MMO and XCO ontologies from automatic processing; these ontologies can be live edited as of now

Mar 28, 2018  v.1.5.39
  removed PW ontology from automatic processing: PW ontology can be live edited as of now

Jan 3, 2018  v.1.5.38
  OboFileGenerator: fixed for DO+ ontology

Dec 29, 2017  v.1.5.37
  transition from RDO to DO+ ontology

Oct 25, 2017  v.1.5.36
  RDO ontology: synonyms from CTD OBO file (source='OBO') are no longer inserted/deleted for RDO terms

Sep 26, 2017  v.1.5.34
  fixed source of CL ontology
  improved parsing of created_by fields for MP,HP ontologies

Sep 21, 2017  v.1.5.33
  gviewer stats loader: bumped up limit of max-annot-count-per-term from 1000 to 2500

Sep 12, 2017  v.1.5.32
  term stats loader for term with filter: rewritten for performance (100x faster)
  split gviewer stats computation to another file

Sep 5, 2017  v.1.5.31
  term stats loader: optimized for better performance

Sep 1, 2017  v.1.5.30
  file parser: extended to allow loading of custom term relations for DO ontology

Aug 30, 2017  v.1.5.29
  DOID mapper: enforced a rule to always map DOID terms to RDO terms
    if a DOID term cannot be mapped by MESH/OMIM id, nor by synonym,
    then it will be mapped to parent terms

Aug 22, 2017  v.1.5.28
  parser: commented out setting comment for custom root terms
        'created by OntologyLoad pipeline to enforce single root for ontology'

Aug 2, 2017  v.1.5.27
  added new banned synonyms

Jul 5, 2017  v.1.5.26
  term stat loader: added CS to list of phenominer ontologies

Jul 3, 2017  v.1.5.25
  doid mapper: fixed bug when deleting stale synonyms
  added chinchilla-species-sources ontology to list of supported ontologies

Jun 30, 2017  v.1.5.24
  term stats loader: added computation of counts for variants
  obo file creator: fixed conversion of 'primary_id' to 'alt_id' synonyms to prevent emission of duplicate synonym lines

Jun 23, 2017  v.1.5.23
  term stats loader: added computation of counts for variants

Jun 8, 2017  v.1.5.22
  term stats loader: added computation of annotation counts for terms for all species (species_type_key=0)

May 26, 2017  v.1.5.21
  term stats loader: added computation of counts of phenominer annotations for male and female strains


Mar 16, 2017  v. 1.5.20
---------------------------
parser: incoming synonyms for CHEBI ontology
   incoming synonyms like '0', '0.0', '234.433', '-2' are skipped from loading;
   they were messing up badly search results into OntoMate text mining tool


Mar 14, 2017  v. 1.5.19
---------------------------
updated download url for HP ontology


Mar 1, 2017  v. 1.5.18
---------------------------
Jeff updated stat computation module: now filters are possible


Jan 10, 2017  v. 1.5.17
---------------------------
sped up loading of big ontologies like CHEBI by moving term-cycle-detection code from data-log-thread to qc-threads
fixed source url for SO and NBO ontology


Jan 3, 2017  v. 1.5.16
---------------------------
added loading of Zebrafish Anatomy (ZFA) ontology into RGD as nonpublic ontology


Dec 20, 2016  v. 1.5.15
---------------------------
strip comments from term names


Nov 7, 2016  v. 1.5.14
---------------------------
fixed NullPointerExceptions in new code dealing with DOIDs


Nov 1, 2016  v. 1.5.13
---------------------------
fixed matching by MESH ids for DOIDMapper


Oct 5, 2016  v. 1.5.11
---------------------------
changed MGI download urls -- per RGDD-1287


Oct 4, 2016  v. 1.5.10
---------------------------
added QC of RS term synonyms: malformed synonyms are reported to curators responsible for RS ontology


Sep 12, 2016  v. 1.5.9
---------------------------
updated source for MP ontology (the old source was dead for 2 months)


Jun 16, 2016  v. 1.5.8
---------------------------
QC: fixed handling of term definitions
DOIDMapper: fixed NullPointerException when handling xrefs with null type


Jun 1, 2016  v. 1.5.7
---------------------------
updated source for NBO ontology (the old source was dead since 3 weeks)


May 17, 2016  v. 1.5.6
---------------------------
obo parser: relations that are not supported by the parses are reported in the summary email,
   and no longer individually, to significantly reduce the size of summary email -- per RGDD-1210
term stats: added computing of 'diagram_count' for pathways -- per RGDD-1206


May 12, 2016  v. 1.5.5
---------------------------
DO ontology: changed source to load richer set of relations (inferred parents) -- per RGDD-1208


May 09, 2016  v. 1.5.4
---------------------------
extended qc: reporting inserted terms that could cause cycles
RDO ontology: reporting terms without accession id


May 05, 2016  v. 1.5.3
---------------------------
code enhanced to be able to use the full featured GO file -- per RGDD-719
1) new relations supported: ends-during, happens-during, starts-during and occurs-in
2) cross-ontology relations are filtered out during loading
3) fixed xref parsing for some more complex cases (containing commas in xref descriptions)


Apr 11, 2016  v. 1.5.2
---------------------------
updated generate_obo_file.sh to use .rgd. instead of .hmgc. domain -- per RGDD-1193


Mar 24, 2016  v. 1.5.1
---------------------------
added MI (molecular interactions) ontology to RGD -- per RGDD-1178


Mar 21, 2016  v. 1.5.0
---------------------------
implemented incremental updates strategy for loading term relationships into ONT_DAG table -- per RGDD-1175


Feb 21, 2016  v. 1.4.13
---------------------------
fixed synonym parsing (skip self-referencing synonyms: where term acc equals to synonym name)


Feb 8, 2016  v. 1.4.12
---------------------------
updated source URL for SO ontology (for 2+ years SO ontology had not been updated)


Feb 7, 2016  v. 1.4.11
---------------------------
FileParser: if incoming term name contains ';' in term name it is being split into a term name
  (the part before semicolon) and synonym(s) (the part after ';')


Jan 14, 2016  v. 1.4.10
---------------------------
DOID mapper:
  rdoTermsNotMatchingDo.txt file also exports count of annotations in RGD


Dec 16, 2015  v. 1.4.9
---------------------------
DOID mapper: now exporting file doTermsMatchingRdo.txt
  rdoTermsNotMatchingDo.txt file exports associated top level RDO diseases


Dec 16, 2015  v. 1.4.8
---------------------------
DOID mapper: fixed a bug in implementation of RULE1 for RDO terms matching by term name or synonym
  rdoTermsNotMatchingDo.txt file exports associated MESH and OMIM ids


Dec 15, 2015  v. 1.4.7
---------------------------
DOID mapper, improved: implemented RULE1 to avoid redundant assignments  of DOIDs
  if a given DO terms is matched to multiple RDO terms, we remove the child terms
  f.e. if DO term matches both [Skin Diseases] and [Skin Diseases Genetic],
       only synonym to [Skin Diseases] will be made
       because [Skin Diseases Genetic] is a child term of [Skin Diseases]
       therefore assignment of this DOID to [Skin Diseases Genetic] is redundant and confusing


Dec 9, 2015  v. 1.4.6
---------------------------
DOID mapper, initial version, done


Nov 18, 2015  v. 1.4.5
---------------------------
-FileParser: improved parsing of excluded synonyms:
   one synonym could be excluded for multiple terms, f.e.
         <entry key="DFNB18" value="OMIM:602092|MESH:C566580" />


Nov 12, 2015  v. 1.4.4
---------------------------
-added 'DO' ontology to the list of ontologies processed in 'run_all.sh' script


Nov 3, 2015  v. 1.4.3
---------------------------
-QC: SynonymManager: fixed a bug in synonym handling causing deletions of synonyms having 2+ same words
  f.e. due to this bug, terms
    'Thoracic Aortic Aneurysms and Aortic Dissections' and 'Thoracic Aortic Aneurysms and Dissections'
    were considered identical (while they weren't) and therefore one of them was being dropped at random


Oct 13, 2015  v. 1.4.2
---------------------------
-DataLoader: protection against insertions of self-referencing dags


Oct 9, 2015  v. 1.4.1
---------------------------
-FileParser: fixed code for handling term merges (when one term in RGD has multiple MESH/OMIM ids
   and there are multiple incoming records to be merged when loading into one)


Oct 6, 2015  v. 1.4.0
---------------------------
-retired RDO_custom.obo terms file (replaced by RGD term edit tool)


Sep 10, 2015  v. 1.3.65
---------------------------
-added loading of xref descriptions


Sep 1, 2015  v. 1.3.64
---------------------------
-fixed run_single.sh script
-FileParser: added handling of source_atlas field for UBERON ontology


Aug 17, 2015  v. 1.3.63
---------------------------
TaxonConstraint module: in addition to refreshing 'only_in_taxon' and 'never_in_taxon' synonyms,
  'Not4Curation' synonyms are generated for those GO terms which violate the above loaded taxon constraints
  (f.e. if a GO term is tagged as 'only_in_taxon Bacteria', this term and all of its child terms are
        tagged as 'Not4Curation', because we do not curate bacteria, only Mammals lineage)


May 11, 2015  v. 1.3.62
---------------------------
FileParser: fixes in handling custom term relationships for RDO ontology


May 6, 2015  v. 1.3.61
---------------------------
TermStatLoader: computes stats for chinchilla, in addition to rat,mouse and human


Apr 15, 2015  v. 1.3.60
---------------------------
FileParser: handles custom term relationships for RDO ontology


Mar 24, 2015  v. 1.3.59
---------------------------
refactored TermStats calculation module
FileParser: "." synonyms, common for CHEBI, won't be loaded anymore


Feb 17, 2015  v. 1.3.58
---------------------------
FileParser: improved handling of excluded synonyms (previously, there was a chance that some synonyms
   that should be excluded, were still loaded)


Feb 11, 2015  v. 1.3.57
---------------------------
QualityChecker: improved loading of RDO term names
  (if incoming RDO term name differs in case from term name in database, the term name is left as it is;
   this rule is to avoid overwriting [Muckle-Wells Syndrome] with [MUCKLE-WELLS SYNDROME]


Jan 27, 2015  v. 1.3.56
---------------------------
FileParser: ", IGNORED" synonyms when loaded have their synonym type set to NARROW


Nov 25, 2014  v. 1.3.55
---------------------------
FileParser: HP ontology: HP:0040005 properties are ignored during loading
  (they are an extended version of definition field)


Nov 21, 2014  v. 1.3.54
---------------------------
FileParser: removed downloading and parsing of files from MESH -- no longer needed


Nov 14, 2014  v. 1.3.53
---------------------------
FileParser: implemented excluded term synonyms
  (incoming synonyms that are present on excluded synonyms list, won't be loaded into database)


Nov 10, 2014  v. 1.3.52
---------------------------
OboFileCreator v.1.2.2: fixed copying of RDO.obo file via data_release -- per RGDD-1008


Oct 29, 2014  v. 1.3.51
---------------------------
TermStatLoader v.2.3.0: compute stats for new columns: RAT_GENES_FOR_TERM, RAT_GENES_WITH_CHILDREN


Oct 27, 2014  v. 1.3.50
---------------------------
OboFileCreator v.1.2.1: no longer duplicate alt_id: lines are emitted (per RGDD-1001); in addition, term synonyms
   are sorted by type and name


Oct 21-22, 2014  v. 1.3.49
---------------------------
CtdMapper v.1.6.0: no longer inserts new RDO terms -- per RGDD-998
MeshDefLoader: merges definitions and synonyms with the incoming CTD terms; called from FileParser
FileParser: merges incoming CTD terms with RDO custom terms, before passing the data to QC
  note: early merging of mesh data and RDO custom terms with incoming CTD terms
      improves quality of loading immensely
   previously loading of RDO custom terms could overwrite the existing terms resulting in unnecessary term updates
     and synonyms inserts and deletions
   previously loading of MESH data could overwrite the existing terms resulting in unnecessary term updates
     and synonyms inserts and deletions
   this is no longer the case! loading is now much more stable

Oct 7, 2014  v. 1.3.48
  QC 1.3.3: SynonymManager can handle terms with null name

Jul 8, 2014  v. 1.3.47
  FileParser v.1.3.4: can now handle empty 'def:' fields

Jul 8, 2014  v. 1.3.46
  CtdMapper 1.5.2: turned off sophisticated code for term upgrade: it was producing wrong results

Jul 8, 2014  v. 1.3.45
  FileParser 1.3.3:
    HP ontology: source url updated
    NBO ontology: added handling of fields "property_value: http://purl.org/dc/elements/1.1/date"
    downloaded OBO files are quick-checked for well-formedness
  StatLoader
    fix: stale terms are not dropped for malformed obo files
  Loader
    fix: stale synonyms are not dropped for malformed obo files

Jun 23, 2014  v. 1.3.44
  FileParser 1.3.2: filtering out comments of some well-known comment types, for UBERON ontology;
    'Not4Curation' synonyms added for GO terms of 'gocheck_do_not_annotate' and 'gocheck_do_not_manual_annotate' subsets;
    added support for new fields for ontology synonyms
  QC 1.3.2: added support for new fields for ontology synonyms
  DL 1.1.1: added support for new fields for ontology synonyms

Jun 18, 2014  v. 1.3.43
  OboFileGenerator v.1.1.5: copying to staging directory is disabled; script copies RDO.obo to the right directory

May 13, 2014  v. 1.3.42
  FileParser v.1.3.1: added parsing of dates in format 'yyyy-MM-dd' in addition to the currently supported format
    yyyy-MM-dd'T'HH:mm:ss'Z' - per RGDD-920

May 5, 2014  v. 1.3.41
  OboFileGenerator v.1.1.4: RDO.obo file is copied to staging directory upon being generated

Apr 8, 2014  v. 1.3.40
  TermStatsLoader v.2.2.1: improved logging of orphaned terms that were made obsolete

Mar 6, 2014  v. 1.3.39
  changed source for HP ontology: now it is using latest stable file

Feb 26, 2014  v. 1.3.38
  FileParser 1.3.0: added handling of UBERON ontology, subset basic

Feb 20, 2014  v. 1.3.37
  TermStatLoader v 2.2: improved code to handle loading of ORDO ontology with acc prefix 'Orphanet:'
  FileParser 1.2.13: added handling of ORDO ontology with acc prefix 'Orphanet:'

Feb 18, 2014  v. 1.3.36
  Manager: removed AnnotationMapper entirely (it was used one time only during transition to CTD/RDO ontology)
  FileParser 1.2.12: improved counting of inserted terms (per ontology)
  QualityChecker 1.3.1: improved counting of inserted terms (per ontology)
  CTDMapper 1.5.1: improved counting of inserted terms (per ontology)

Jan 20, 2014  v. 1.3.35
  TaxonConstraints module: added loading of taxon constraints for GO terms

Jan 8, 2014  v. 1.3.34
  MeshDefLoader module v. 1.2.2: config file updated to use MESH 2014 database instead of MESH 2013 database- per RGDD-866

Dec 3, 2013  v. 1.3.33
  turned off additivity for meshDef logger (its entries won't go into root.log anymore);
  changed logging level to info for meshDef logger (only logging stats and changes)

Nov 26, 2013  v. 1.3.32
  turned off additivity for ctdMapper logger (its entries won't go into root.log anymore)

Nov 4, 2013  v. 1.3.31
  version 1.2.11 of FileParser module:
    encoding override could be specified for every ontology

Oct 30, 2013  v. 1.3.30
  version 1.3 of QualityChecker module:
    1.improved logging for inserts: no longer inserted regular terms will be logged in without full term information
    2. rolled back feature 1 -- too much problems in implementing it
  version 1.5 of CTDMapper module:
    more relevant logging for OMIM mapped ids

Oct 28, 2013  v. 1.3.29
  version 1.2 of QualityChecker module:
    added logging of changed term names into file termNameChanged.log

Oct 22, 2013  v. 1.3.28
  version 1.2.10 of FileParser module:
    do not list all terms skipped in the summary email - give only the summary
    detailed info should go to the log file

Sep 16, 2013  v. 1.3.27
  version 1.4 of ctdFileMapper module:
    better matching by OMIM synonyms (elimination of spurious inserts of new terms)

August 22, 2013  v. 1.3.26
  version 1.2.9 of FileParser module:
    added parsing of xdbrefs for term definitions
  version 1.1 of QualityChecker module:
    added qc of dbxrefs against database
  version 1.1 of DataLoader module:
    added loading and logging of dbxrefs (inserts and deletes)
  version 1.1.3 of oboFileGenerator module:
    added export of dbxrefs for tem definitions

August 21, 2013  v. 1.3.25
  version 1.1.2 of oboFileGenerator module:
    write out fields 'created_by:' and 'creation_date:'

July 23, 2013  v. 1.3.24
  version 1.2.8 of FileParser module:
    if ontology id of processed ontology cannot be validated against database, error message is printed out
    instead of crashing of the entire application

July 18, 2013  v. 1.3.23
  version 1.1.1 of oboFileGenerator module:
    generate synonyms conforming to obo file format 1.2 (not uses deprecated synonyms exact_synonym, etc)
  version 1.2.7 of FileParser module:
    user can specify in properties file which ontologies should use exact synonym matching when loading synonyms
    "ISO-8859-1" encoding is used when reading obo files to prevent loading of garbage characters (RS ontology)

July 17, 2013  v. 1.3.22
  version 1.1.0 of oboFileGenerator module:
  obo file for any ontology could be generated;
  obo file header is read from database table ONTOLOGIES field OBO_HEADER

May 22, 2013  v. 1.3.21
  version 1.2.6 of fileParser module:
  RDO_custom.obo file processing: new synonyms for non-custom RDO terms could be added

Mar 19, 2013  v. 1.3.20
  version 1.2.5 of fileParser module:
  added parsing of 'date' and 'note' fields -- currently present in NBO ontology

Feb 22, 2013  v. 1.3.19
  RDO ontology: synonyms ending with ', INCLUDED' or ', FORMERLY' will be fixed before loading - per RGDD-679
   also for 'RDO' ontology synonyms are split into multiple synonyms when ';' character is encountered

Feb 21, 2013  v. 1.3.18
  orphaned obsoleted terms are logged into file 'obsoletedTerms.log'

Feb 20, 2013  v. 1.3.17
  omim_gene_assoc synonyms are no longer generated for terms with OMIM IDs - per RGDD-677

Feb 12, 2013  v. 1.3.16
  CTDMapper module v. 1.2: allows for upgrade of OMIM-only terms into MESH+OMIM terms  - per RGDD-646

Jan 29, 2013  v. 1.3.15
  Fixed handling of duplicate synonyms
  MeshDefLoader module v. 1.2.0: updated to avoid insertion of duplicate term synonyms

Jan 23, 2013  v. 1.3.14
  MeshDefLoader module v. 1.0.1: config file updated to use MESH 2013 database instead of MESH 2012 database- per RGDD-652

Nov 16, 2012  v. 1.3.13
  TermStats module fixed to compute phenominer data for gviewer properly - per RGDD-594

Nov 12, 2012  v. 1.3.12
  QC module automatically removed pseudo duplicate synonyms: per RGDD-542
  'FSGS1 [synonym]' and 'FSGS1 [exact_synonym]' -->  'FSGS1 [exact_synonym]
  'FSGS1 [synonym]' and '"FSGS1 [synonym]"'     --> 'FSGS1 [synonym]'

Nov 9, 2012  v. 1.3.11
  TermStats module fixed to compute phenominer data for gviewer properly;
  (stats for phenominer data must always computed as term-only) - per RGDD-594

October 31, 2012  v. 1.3.10
  Incoming Reactome xref_analog synonyms are synced with synonyms in RGD. If a Reactome synonym
  is no longer present in incoming data, it is removed from RGD database.  - per RGDD-599

October 26, 2012
  Automatic generation of matching gene symbols as synonyms of type 'omim_gene_assoc'
  for terms having OMIM synonyms (currently applies only to RDO ontology)   - per RGDD-595

October 18, 2012
  Fixed improper generation of new RDO ids when custom RDO terms are present - per RGDD-589

August 21, 2012
  Improved script run_all.sh

August 14, 2012
  Added TermSynonymCleaner module. It is run by specifying command line option "-cleanup_synonyms".
    It cleans duplicate synonyms from database and logs them into a separate log file "synonym_cleaner.log"

July 30, 2012
  FileParser module v 1.2.4: custom terms could be loaded from RDO_Custom.obo file.
    This included also loading of new relationships between existing terms and /or
    between custom and existing terms. [RGDD-333]

June 21, 2012
  FileParser module v 1.2.3: changed root term for SO ontology from SO:0000000 to SO:9999999;
    SO:0000000 appears in official SO.obo file as obsolete term, so we had clash with root term
    for SO ontology supplied in the config file

May 29, 2012
  FileParser module v 1.2.2: fixed dropping of old dag for GO ontology