Weekly Curation Updates

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Weekly Curation Updates (03/04/2011)

1.Combinational relationships and Complex disease terms

  • Deleted all the links that used the relationship "complicated_by". [Completed]
  • Obsoleted the DO terms that combine 2 disease terms with conjunctions like "and", "or", "with" etc.(In Progress)

2.Multiple inheritance in disease by infectious agent node

  • Checked/updated the textual definitions, if they have the right primary and seconadry parents.
  • Added secondary parent in the textual definition and deleted the link between the term and secondary parent. (Completed)

3. DO-OMIM match review

  • Deleted all OMIM:MTHU dbxrefs from DO_logical_def file, as they do not represent exact matches. (Completed)
  • Checking if MIM ids in the OMIM dbxrefs (with OMIM phenotype record) match with their corresponding DO term. If they do not match, then finding the right DO term for that particular OMIM dbxref. (In Progress)
  • Adding OMIM term name as a synonym, if its missing. (In Progress)
  • Docmenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)
  • Adding all MIM ids of a phenotype series as dbxrefs under their corresponding DO term (for which "Union" will be used later). (In Progress)

Weekly Curation Updates (03/11/2011)

1. DO-OMIM match review (from last week completed)

2. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Docmenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

3. Immune system diseases

  • Updating Immune system diseases. (In Progress)

4. Bone diseases

  • Defining bone diseases. (In Progress)

Weekly Curation Updates (03/18/2011)

1. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

2. Syndrome

  • Checking if terms under "syndrome" node are actually syndromes or real diseases. If they are real diseases, then moving them under appropriate parents. (In Progress)

3. Genetic disease and medical disorder

  • Checking if "genetic disease" and "medical disorder" terms match with OMIM phenotypes and adding matched phenotype MIM ids as dbxrefs. (Completed)

4. Bone diseases

  • Defining bone diseases. (In Progress)

Weekly Curation Updates (03/25/2011)

1. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

2. Syndrome

  • Checking if terms under "syndrome" node are actually syndromes or real diseases. If they are real diseases, then moving them under appropriate parents. (Completed)

3. Bone diseases

  • Defining bone diseases. (In Progress)

4. OMIM records across different ontologies of interest

  • Creating an excel spreadsheet to map OMIM phenotype records within different ontologies. (In Progress)

Weekly Curation Updates (04/01/2011)

1. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

2. Logical definitions

  • Adding logical definitions in "disease of anatomical entity" and "cancer" nodes referring to terms from FMA (In Progress)
  • Adding logical definitions in "viral infectious disease" node referring to terms from NCBITaxonomy (In Progress)
  • Replaced "has_agent" relation with "has_physical_basis_in" relation in HumanDO_xp.obo file.

3. Bone diseases

  • Defining bone diseases. (In Progress)

Weekly Curation Updates (04/08/2011)

1. Logical definitions

  • Replaced "results_from" relation with "has_material_basis_in" relation in HumanDO_xp.obo file.
  • Replaced "has_physical_basis_in" relation with "has_material_basis_in" relation in HumanDO_xp.obo file.
  • Removed secondary parents from the defintions. (Completed)
  • Added logical definitions in "viral infectious disease" node linking to NCBITaxonomy terms. (In Progress)
  • Added logical definitions linking DO terms with FMA terms using located_in relation. (In Progress)

2. Reasoner Redundant links

  • Fixed reasoner redundant links.

3. DO-GO linkage

  • Added logical definitions linking DO terms with GO biological precess terms using "realized_by_supression_with " relation.

Weekly Curation Updates (04/15/2011)

1. Logical definitions

  • Added logical definitions in "viral infectious disease" node linking to NCBITaxonomy terms. (In Progress)
  • Added logical definitions linking DO terms with FMA terms using located_in relation. (In Progress)
  • Cleaning up some placeholder terms in viral infectious disease , parasitic helminthiasis infectious disease, fungal infectious disease and bacterial infectious disease nodes. (In Progress)

2. Reasoner Redundant links

  • Fixed reasoner redundant links.

Weekly Curation Updates (04/22/2011)

1. Logical definitions

  • Added logical definitions in "viral infectious disease" node linking to NCBITaxonomy terms. (Completed)
  • Cleaning up some placeholder terms in viral infectious disease , parasitic helminthiasis infectious disease, fungal infectious disease and bacterial infectious disease nodes. (In Progress))

2. Reasoner Redundant links

  • Fixed reasoner redundant links.

3. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

Weekly Curation Updates (04/29/2011)

1. Logical definitions

  • Cleaning up some placeholder terms in bacterial infectious disease node. (Completed)

2. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

3. NCBITaxonomy Bacteria slim

  • Creating NCBI Taxonomy bacteria slim for further use in adding logical definitions in bacterial infectious disease node.

Weekly Curation Updates (05/06/2011)

1. Logical definitions

  • Adding logical definitions in bacterial infectious disease node linking DO terms to FMA and NCBI Taxonomy. (Completed)

2. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

3. Reasoner Redundant links

  • Fixed reasoner redundant links.

4. Multiple parentage

  • Deleted multiple parentage for all the terms that have >= 3 parents.

Weekly Curation Updates (05/13/2011)

1. NCBITaxonomy Fungi slim

  • Creating NCBI Taxonomy Fungi slim for further use in adding logical definitions in fungal infectious disease node.

2. Logical definitions

  • Adding logical definitions in "fungal infectious disease" node linking DO terms to NCBITaxonomy terms. (In Progress)

3. "Disease of cellular proliferation" node reorganization

  • Disease of cellular proliferation node is organized into 3 top level nodes - 1)malignant neoplasm 2)pre-malignant neoplasm 3)benign neoplasm.
  • Malignant neoplasm is organized by 1)organ system cancer 2) cell type cancer
  • Malignant neoplasm node is organized based on anatomical location.
  • Most of "sarcoma" terms have been moved to their respective anatomical location cancer nodes.
  • Cleaning up relapsing cancer terms, placeholder terms and compound terms(terms which are combination of 2 types of cancers).

Weekly Curation Updates (05/20/2011)

1. Logical definitions

  • Adding logical definitions in "fungal infectious disease" node linking DO terms to NCBITaxonomy terms. (Completed)
  • Adding logical definitions in "fungal infectious disease" node linking DO terms to FMA terms.

2. NCBITaxonomy Protozoa slim

  • Creating NCBI Taxonomy Protozoa slim for further use in adding logical definitions in parasitic protozoa infectious disease node.

3. "Disease of cellular proliferation" node reorganization

  • Moving "carcinoma" terms to their respective anatomical location cancer nodes. (In Progress)
  • Cleaning up relapsing cancer terms, recurrent cancer terms, placeholder terms and compound terms(terms which are combination of 2 types of cancers).
  • Moving "neoplasm" terms under bening neoplasm node.
  • Getting rid of multiple parentage of cancer terms.
  • Replacing "malignant neoplasm" with "cancer".
  • Cleaned up "respiratory system cancer" and "respiratory system neoplasm".

Weekly Curation Updates (05/27/2011)

1. NCBITaxonomy Annelida and Arthropoda slim

  • Created NCBI Taxonomy Annelida and Arthropoda slim for further use in adding logical definitions in parasitic ectoparasitic infectious disease.

2. Logical definitions

  • Added logical definitions in "parasitic protozoa infectious disease", "parasitic ectoparasitic infectious disease" and "parasitic Ichthyosporea infectious disease" nodes linking DO terms to NCBITaxonomy terms. (Completed)
  • Added logical definitions in "parasitic protozoa infectious disease" node linking DO terms to FMA terms. (In Progress)

3. "Disease of cellular proliferation" node reorganization

  • Moved terms under "transitional cell carcinoma" and "squamous cell carcinoma" to their respective anatomical location cancer nodes. (Completed)
  • Getting rid of multiple parentage of cancer terms.
  • Cleaned up "gastrointestinal system cancer", "gastrointestinal system neoplasm", "urinary tract cancer" and "urinary tract neoplasm".

4. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

Weekly Curation Updates (06/03/2011)

1. "Disease of cellular proliferation" node reorganization

  • Moved carcinoma, sarcoma and blastoma under malignant neoplasm node and added textual definitions for these terms.
  • Moved lymphoma under hematologic cancer node and updated the definition.
  • Added textual definitions for malignant neoplasm, benign neoplasm and pre-malignant neoplasm.
  • Cleaned up skin neoplasm and skin cancer nodes. Moved all the benign skin tumors under skin neoplasm and malignant skin tumors under skin cancers. Got rid of multiple parentage in these nodes. Fixed the nomenclature.

2. Logical definitions

  • Adding textual and logical definitions in bacterial infectious disease node. Logical definitions were added linking DO terms to FMA. (In Progress)

3. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

Weekly Curation Updates (06/10/2011)

1. "Disease of cellular proliferation" node reorganization

  • Renamed "malignant neoplasm to "cancer".
  • Cleaned up papillary epithelial neoplasm, oncocytic neoplasm, mesonephric tumor, serous neoplasm, mucinous tumor nodes.
  • Moved squamous cell carcinoma and transitional cell carcinoma under carcinoma.
  • Cleaning up adenocarcinoma. (In Progress)

2. Logical definitions

  • Adding textual and logical definitions in bacterial infectious disease node. Logical definitions were added linking DO terms to FMA. (In Progress)

3. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

Weekly Curation Updates (06/17/2011)

1. "Disease of cellular proliferation" node reorganization

  • Cancer node has been divided into 2 top level nodes 1)cell type cancer (based on the type of cell from which cancer develops) 2)organ system cancer (based on the organ in which the cancer starts)
  • Cleaned up adenocarcinoma and moved the node under carcinoma.
  • Textual definitions have been added to all the top level nodes of cancer.
  • Nevus/nevi terms, metastatic cancer/non metastatic cancer/secondary/disseminated/recurrent cancer/relapsed cancer terms have been deleted.
  • All primary cancer terms have been merged with their proper parents.

2. Logical definitions

  • Adding textual and logical definitions in bacterial infectious disease node. Logical definitions were added linking DO terms to FMA. (In Progress)

3. New OMIM phenotypes

  • Adding new OMIM phenotypes that are not in the DO.(In Progress)
  • Documenting that the OMIM dbxref has been checked in the comments field of the obo file. (In Progress)

Weekly Curation Updates (06/24/2011)

1. "Disease of cellular proliferation" node reorganization

  • Worked on neuronal and glio-neuronal neoplasm node.
  • Cleaning up neuroepithelial neoplasm under glandular and epithelial neoplasm (In Progress)

2. Logical definitions

  • Adding textual and logical definitions in bacterial infectious disease node. Logical definitions were added linking DO terms to FMA. (In Progress)

Weekly Curation Updates (07/01/2011)

1. Logical definitions

  • Added textual and logical definitions in bacterial infectious disease node. Logical definitions were added linking DO terms to FMA. (Completed)

2. "Disease of cellular proliferation" node reorganization

  • Cleaned up "carcinoma" node. Added textual definitions to the child terms.(Completed)
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