1. Organism CDE Standard Candidate VCDE, January 22, 2008 VCDE Small Group: Riki Ohira, Dianne Reeves, Mukesh Sharma, Grace Stafford, Baris Suzek, Lynne Wilkens (Lead)

2. Organism This set of standards was proposed by the Information Representation Working Group (IRWG) of the ICR workspace Set of seven CDEs Approved in ICR

3. Taxonomy Taxonomy is defined as: theories and techniques of naming, describing, and classifying organisms, the study of the relationships of taxa, including positional changes not involving changes in the names of taxa. caBIG applications use taxonomy to provide Classifications of great explanatory value in most branches of biology. Allows comparisons between “similar” or “different” organisms as defined by their relative location in the taxonomic tree. Classification is now done on the molecular level taxonomic classification provides a rough way to evaluate the genetic background in model organisms.

4. Key Taxonomy Resources IRWG reviewed numerous taxonomies are available in the literature. NEWT, the Integrated Taxonomic Information System (ITIS), and the National Center for Biotechnology Information (NCBI) taxonomy database The NCBI taxonomy seems most appropriate for caBIG because: 1.Maps to genetic sequence information. 2.It is widely used by other databases at NCBI and in the scientific community. 3.It is updated and curated. 4.It is widely used in other caBIG object models. 5.Many concepts and names already exist in the EVS system at NCI.

5. Organism Models used in caBIG

6. ICR Proposal The goal is to map biological samples to NCBI’s taxonomy and obtain a complete lineage and additional info on the organism. Want to map to the lowest node in the taxonomy (i.e. strain, isolate) Recommend the following to be part of CDE: NCBI Taxonomy ID required if available. Organism Scientific Name be required. Organism Common Name suggested. Other information like taxon and lineage is nice but can be obtained with information above.

7. New Model of Organism CDE

8. NCBI information Mus musculus Taxonomy ID: 10090 Genbank common name: house mouse Rank: species Genetic code: Translation table 1 (Standard) Mitochondrial genetic code: Translation table 2 (Vertebrate Mitochondrial) Other names: common name:mouse includes:transgenic mice includes:nude mice includes:LK3 transgenic mice includes:Mus sp. 129SV misnomer:Mus muscarisTranslation table 1 (Standard)Translation table 2 (Vertebrate Mitochondrial) Lineage( full )Lineage cellular organisms; Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa; Bilateria; Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata; Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii; Tetrapoda; Amniota; Mammalia; Theria; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Muscellular organismsEukaryotaFungi/Metazoa groupMetazoaEumetazoaBilateria CoelomataDeuterostomiaChordataCraniataVertebrataGnathostomata TeleostomiEuteleostomiSarcopterygiiTetrapodaAmniotaMammaliaTheria EutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridae MurinaeMus

9. Organism Identification CDEs Candidate Standards are registered in the caDSR (http://umlmodelbrowser.nci.nih.gov/umlmodelbrowser/) and may be found in the Browser tree under caBIG/Organism Identification

10. Organism CDEs Organism National Center for Biotechnology Information Taxonomy Identifier java.lang.Long 2342465v1.0 caBIG A living thing, such as an animal, a plant, a bacterium, or a fungus._Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. (http://www.ncbi.nlm.nih.gov/):The theories and techniques of naming, describing, and classifying organisms, and the study of the relationships of taxa. (from On-line Medical Dictionary):One or more characters used to identify, name, or characterize the nature, properties, or contents of a thing._Value Domain for java language Long datatype. Organism National Center for Biotechnology Information Taxonomy Identifier 2342291v1.0 caBIG Object = Organism (C14250) Property = Identifier (C25364) P. Qualifier = National Center for Biotechnology Information (C45799) P. Qualifier + Taxonomy (C25364) Java.lang.Long To be changed to: Representation Type Non-Enumerated

11. Organism CDEs Organism Scientific Name java.lang.String 2223784v3.0 caCORE A living thing, such as an animal, a plant, a bacterium, or a fungus._The name applied to a plant, animal, or other organism, according to the Codes of Nomenclature, consisting of a Genus and species._Value Domain for java language String datatype. Organism Scientific Name 2223629v3.0 caCORE Object Class = Organism (C14250) Property = Scientific Name (C43459) Java.lang.String To be changed to: Text Non-Enumerated Organism Common Name java.lang.String 2223787v3.0 caCORE A living thing, such as an animal, a plant, a bacterium, or a fungus._Widely known or encountered.:The words or language units by which a thing is known._Value Domain for java language String datatype. Organism Common Name 2223629v3.0 caCORE Object Class = Organism (C14250) Property = Name (C42614) P. Qualifier = Common (C43461) Java.lang.String To be changed to: Text Non-Enumerated

12. Organism CDEs Organism Taxonomy Rank Taxon Rank Name 2590793v1.0 A living thing, such as an animal, a plant, a bacterium, or a fungus._The theories and techniques of naming, describing, and classifying organisms, and the study of the relationships of taxa.:A relative status as compared to others within a group._A group or category, at any level, in a system for classifying plants or animals. (On-line Medical Dictionary)_A relative status as compared to others within a group._The words or language units by which a thing is known. Organism Taxonomy Rank 2590787v1.0 caBIG Object Class = Organism (C14250) Property = Rank (C48904)P. Qualifier = Taxonomy (C17469) Taxon Rank Name 2526618v2.0 caBIG Enumerated (see attached table of permissible values)

13. Permissible Values for Taxon Rank See Organism_TaxonPVs.doc

14. Organism CDEs Organism Additional Name Value java.lang.String 2590797v1.0 caBIG Any individual living thing.:Added; extra; further.:The words or language units by which a thing is known._The information contained in a data field._Generic value domain for a java datatype that is a class that represents character strings. Organism Additional Name Value 2590791v1.0 caBIG Object Class = Organism Additional Name (C14250: C25406: C42614) Property = Value (C49100) Java.lang.String To be changed to: Text Non-Enumerated Organism Additional Name Source java.lang.Long 2590796v1.0 caBIG Any individual living thing.:Added; extra; further.:The words or language units by which a thing is known._Where something is available._Generic value domain for a java datatype that is a class that represents character strings. Organism Additional Name Source 2590796v1.0 caBIG Object Class = Organism Additional Name (C14250: C25406: C42614) Property = Source (C25683) Java.lang.Long To be changed to: Representation Type Non-Enumerated

15. Organism CDEs Organism Additional Name Comment java.lang.String 2590798v1.0 caBIG Any individual living thing.:Added; extra; further.:The words or language units by which a thing is known._A written explanation or criticism or illustration that is added to a book or other textual material._Generic value domain for a java datatype that is a class that represents character strings. Organism Additional Name Comment 2590792v1.0 caBIG Object Class = Organism Additional Name (C14250: C25406: C42614) Property = Comment (C14250) Java.lang.String To be changed to: Text Non-Enumerated

16. First Use of CDE Standards Criteria See Checklist Meet almost every requirement Small group recommend changing JAVA types to Generic

17. Next steps Questions? Vote in VCDE to send to caBIG for comment?