LaRon Hughes is focusing on the cancer node of the Disease Ontology.
- The first objective is to restructure the cancer node to avoid redundancy in terms
- The second objective is to remove or edit terms that contain factors that are not consistent with the style guide (see Style Guide).
- The third objective is to create textual definitions from sources such as Wikipedia and the National Cancer Institute.
- The fourth objective is to create logical definitions that will allow the Disease Ontology to effectively communicate with other ontologies on a computational level. This process will involve mireoting the Disease Ontology with the Cell Ontology and the Functional Model Organism (FMA) ontology.
- The fifth objective is to reduce the number of cancer node terms that have multiple parentage. The creation of logical definitions will help reduce the number of multiple parentage terms through the inclusion of these terms in the logical definition.
- The sixth objective is to organize the structure of the cancer node to accommodate the needs of the disease ontology community. (Cancer Node Organization)
- Defining terms in "cancer of the nervous system" node
- Restructuring the "hematologic cancer" node
- Creating textual definitions for top level terms in the cancer node
- Editing or removing terms to be consistent with the style guide (see Style Guide)
- Create textual definitions for lower level terms.
- Create logical definitions for terms in the cancer node.
- Reduce the number of terms that have multiple parents.
Disease by Infectious Agent Node Curation
Suvarna Nadendla is focusing on the infectious disease node of the disease ontology.
- All the terms of respiratory system infectious disease node have been defined as per the Disease Ontology definition format and their parentage has been corrected. The diseases under this node are organized based on the anatomical structures that are infected by the pathogens like lower respiratory infectious disease and upper respiratory infectious disease. Some of the terms have IDs of related anatomical structures from FMA as dbxrefs. Complex terms containing "and" and "with" have been taken care of.
- All the terms of gastrointestinal system infectious disease node have been defined and their parentage has been corrected. The diseases under this node are organized based on the anatomical structures that are infected by the pathogens. Some new infectious diseases have been added that were not in DO before.
- Reorganized parasitic infectious disease node. Before, the node was organized based on the anatomical structures infected by parasites. Now, the node is structured based on the taxonomical classification of the parasites causing the disease. There are four major groups of parasites, such as protozoans, helminths, ectoparasites and stramenopiles.
- Reorganized fungal infectious disease node. Before, the node was organized based on the anatomical structures infected by fungi and also based on the site of infection (like cutaneous, subcutaneous, superficial and systemic mycosis). Now, the primary axis of categorization is site of infection by the fungal pathogens, which is further categorized based on the taxonomical classification of these fungi (Eg: subcutaneous mycosis -> subcutaneous ascomycota mycosis ->chromoblastomycosis). I started implementing the new textual definition format for defining terms under fungal infectious disease node. For details about the new textual definition format, please visit (Relations in DO).
- Created 2 Subsets: tick-borne infectious disease and zoonotic infectious disease. Worked on tick-borne infectious disease node and zoonotic node. The terms under these nodes have been check marked for the Subsets that they belong to and are moved to their proper parents.
- Reorganized bacterial infectious disease node. Before, the node was organized into families of bacterial pathogens grouped under either Gram positive or Gram negative infectious disease nodes. Now, the primary axis of categorization is the pathogenicity of the bacterial pathogens - 1)primary bacterial infectious disease (diseases caused by bacterial pathogens in healthy individuals) 2)commensal bacterial infectious disease (diseases caused by virulent bacterial pathogens which are part of the normal human flora)and 3)opportunistic bacterial infectious disease(diseases caused by bacterial pathogens in immunocompromised individuals). Each of this node is further classified into taxonomic families of the bacterial pathogens - Eg: Anaplasmataceae infectious disease.
Reorganize viral infectious disease node.
Start adding logical definitions to all the terms. To mireot terms from Cell Ontology and FMA.
Lynn worked on the re-organization of disease by infectious agent node.
There are 3 major areas for an infectious disease,
- body system infectious disease Eg:gastrointestinal system infectious disease
- pathogen infectious disease Eg:bacterial, fungal, parasitic, viral infectious disease
- transmission infectious disease Eg:zoonotic infectious disease, sexually transmitted infectious disease, tick-borne infectious disease
In DO, the disease by infectious agent node was re-oraganized into 4 classes,
1) body system infectious disease: Consists of disease terms related to a particular body system
2) systemic infectious disease: Consists of bacterial, fungal, parasitic, viral infectious diseases
3) tick-borne disease: Consists of diseases transmitted by ticks
4) zoonotic infectious disease: Consists of diseases transmitted from animals to humans
To retain the information about the transmission methodology(sexually transmitted, tick-borne and zoonotic), it was decided to create Subsets for each transmission methodology and and have the terms check marked for a Subset that they belong to.
A new "Subset" (previously called Category) sexually transmitted infectious disease has been created. The sexually transmitted infectious disease node has been removed. All the disease terms that were under this node, are now moved to their proper parents and are assigned to the Subset-sexually transmitted infectious disease. The tick-borne disease and zoonotic infectious disease nodes have been removed after moving the terms under them to their proper parents.
Temp Holding Node Cleanup
Cleaned up temp holding node with 422 terms(as of 4/6/2010). All the temp holding terms are manually examined and are either obsoleted or moved under a proper parent term, following general guidelines for curation. A new "disorder" node has been created to accomodate all the terms that are not diseases but disorders. The "disorder" node has been categorized into 7 child nodes - behavioral, developmental, emotional, functional, genetic, mental and physical disorder.
The general guidelines that are followed to curate the temp holding node,
1) Checking if a term has any active parents.
2) Obsolete terms that are not diseases but are symptoms.
3) Obsolete terms that are just placeholders but not real diseases.
4) Moving terms with OMIM xrefs under a proper parent.
5) Changing a good upper case temp term to lower case.
3 Downloadable DO files
There are 3 DO files that can be dowloaded from SourceForge. The files include the regular HumanDO.obo; the HumanDO_no_xrefs.obo that excludes xrefs, and the DO_logical_def.obo file which includes logical definitions.
Self Cross-Products in the DO
We started adding self cross-products with in the DO. This facilitates us to get rid of multiple parentage of the terms. We implemented this with AIDS-related diseases using complicated_by relation to link with acquired immunodeficiency syndrome.
Adding logical definitions to the terms in the DO
Currently, we are creating logical definitions for terms within the viral infectious disease and cancer nodes. These are located in the DO_logical_def.obo file. The curators are actively working on this file to edit/add information on a daily basis. These logical definitions reference the following ontologies: Foundational Model of Anatomy (FMA), Human phenotype ontology (HPO), Cell type (CL), Pathogen transmission (TRANS), and other OBO Foundry candidate ontologies. The DO_logical_def.obo file is converted to the HumanDO.obo file, by running a perl script at the end of each day, which will get rid of all the logical definitions and terms from other ontologies, leaving only the DOIDs and DO terms.
HumanDO.obo file without xrefs
The HumanDO.obo file is converted to HumanDO_no_xrefs.obo file, by running a perl script at the end of each day, which will get rid of the xrefs of each term in the file.