EXCELL FILE FILLING GUIDELINE How to fill the most important columns: - Term name: whatever - CTO id: CL:nnnnnnn - Ploidy: PATO:0001394 (have a look under PATO:0001374) - Morphology: n/a or PATO:nnnnnnn - Cellular component: GO:nnnnnnn. If more than one: GO:nnnnnnn ; GO:nnnnnnn ; GO:nnnnnnn - Size: I have added a Value Partition, so you should use the terms "Large", "Medium" or "Small". We can define later what each of those means (e.g. < 10 micr). - Germ line: "Somatic" or "Germline" - Nucleation: instead of putting a number use Pato Ids (multinucleate, mononucleate, anucleate): PATO:0001908, PATO:0001407, PATO:0001405. - Process: GO:nnnnnnn. If more than one: GO:nnnnnnn ; GO:nnnnnnn ; GO:nnnnnnn - Process comment: whatever - Lineage: for lineage, it's preferable that you simply put the CL id of the develops_from filler from cell.obo (e.g. CL:0000002). Transitivity (eg classifying a cell as having a mesodermal origin) should do the rest, as shown in the Oxford meeting. Add a CL id only if the term itself has got a develops_from relation. For example, hypertrophic chondrocyte does not have a develops_from relation, chondrocyte does ( develops_from chondroblast) but as it is a subclass of chondrocyte, hypertrophic chondrocyte will "inherit" it so if we assert it is redundant. If more than one: CL:nnnnnnn ; CL:nnnnnnn ; CL:nnnnnnn - Organism: organism names are automatically extracted and added to the main ontology from Cell Type, so putting any of those in the tab file should be fine (you can request a new organism to me): Nematoda_and_Protostomia Arthopoda Vertebrata Mus Endoptyeygota Mycetozoa Arthropoda Diptera Nematoda Fungi Insecta Animalia Plantae Viridiplantae Actinopterygii_and_Amphibia Mammalia Protostomia Aves Mycetozoa Amphibia Embryophyta Mollusca Annelida Marsupialia Reptilia Danio_rerio - Organism comment: whatever - Potentiality: I have added a class called TerminallyDifferentiated cell under cell potentiality (pato), so putting "Terminally differentiated" in the tab file is fine. For the rest use pato ids (eg PATO:0001402). - Anatomy: use a FMA id, e.g.: FMA_74627. If more than one: FMA_74627 ; FMA_74627 ; FMA_74627 - MOS equivalent: use any Manchester OWL syntax expression, it will be added as an equivalent class. This column has been added for the intermediate nodes, cause some need very specific axioms. For example: ro:located_in some fma:FMA_49158 and ro:located_in some fma:FMA_9596 and ro:participates_in some go:GO_0006936. Note that you need to use qualified names cause we are working with imported ontologies (ro, go, fma, cto). to get familiar with he namespaces open cto_norm.owl and resolve the imports. - MOS necessary: same as MOS equivalent but it will be added as a necessary condition. General comments: - Use always term id, eg "PATO:0001394" instead of "diploid", and only id, eg "GO:0032940" instead of "GO:0032940 : secretion by cell". - "n/a" is fine when you don't know what to put. - For various IDs, semicolon with spaces: GO:002456 ; GO:0021700 ; GO:0032940. - Try to limit comments to the "comments" column of each attribute, so for example Organism Organism comment animal (that sweats) Should be Organism Organism comment animal (that sweats)