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FlyBase includes
Core vocabularies:
Phenotypic class (fbcv.obo) Anatomy (fly_anatomy.obo, GO)
Phenotypes are associated with alleles using controlled vocabularies in conjunction with controlled syntax
Phenotype Ontology Meeting Cold Spring Harbor November 19-20th, 2005
Phenotypic class: neuroanatomy defective | recessive Phenotype manifest in: chordotonal organ Phenotype manifest in: midline glial cell
Genetic interaction: suppressor | dominant, visible { argosGMR.PC } Genetic interaction: suppressor | dominant, eye { argosGMR.PC } Genetic interaction: enhancer | dominant, visible { Shs.sev } Genetic interaction: enhancer | dominant, eye { Shs.sev }
Phenotype Ontology Meeting Cold Spring Harbor November 19-20th, 2005
Numbers
Single mutant phenotype statements:
Phenotypic class: 86,153 Anatomy: 81,438
Total phenotypic data lines including free text: 397,821
more
Genetic interaction statements:
Phenotypic class: 35,825 Anatomy: 39,686
Total multiple mutant phenotype lines including free text: 131,208
The Experiment:
9) Now each MOD should try to annotate 50 objects using PATO, and swop those around . . . Everyone do 50 units include aspects of assay, etc/
The Questions:
1: Can the Phenotype Ontology represent all the controlled data that FlyBase allele records include? 2: Can the Phenotype Ontology reduce the amount of free text information in FlyBase allele records?
3: Is the proposed system efficient enough for curators for production database use?
4: Is the end product of this type of curation useful to biologists?
The Methods:
1. Identify candidate data-rich alleles select annotation from one reference 2. Re-annotate with Phenotype Ontology System 3. Identify a. Structural problems? b. Vocabulary problems? c. Practical problems?
asl 1 FBal0030521
current ly inclu d es th e follow in g da ta, att ribu ted to: FBrf0104411 == Bonac corsi et al., 1998, J. Cell Biol. 142(3): 751--761 Phenotypic class: (with asl2) viable Phenotypic class: (with asl3) viable Phenotypic class: male ster ile | recessive Phenotypic class: femal e sterile | recessive Phenotype manifest in : Ne ben ker n d er ivat ive Phenotype manifest in : onion stag e sper mat id Phenotype manifest in : onion stag e sper mat id & nuc le us Phenotype manifest in : (with asl2) sper ma tocyte & aster Phenotype manifest in : (with asl3) sper ma tocyte & aster Phenotype manifest in : first meiotic m etapha se | mal e Phenotype manifest in : first meiotic anaphas e | m ale as l2/ asl1an d asl3/ asl1 anima ls ar e viab le . On ion stage sper mat ids from homoz yg ous mal es hav e nuc le i an d nebe nkern of var iou s sizes. H omoz yg ou s, asl2/ asl1 and asl 3/as l1 sperm atoc ytes are com pletely de void of aster s. Homoz yg ous sper mat ocytes hav e m orpho logicall y no rma l centriole s. How eve r, cen triole separa tion is abno rma l; some nebe nkern are associat ed wit h tw o cent rioles instead of on e as in wild -typ e. Prom et aphas e I, Ontology Meeting m etap h ase I and Phenotype ear Cold ly anap hase I ap pear to la st lon ger Spring Harbor in homoz yg ous testes than in wild -typ e." November 19-20th, 2005
asl 1 FBa l0030521 Usin g Obser vable + attribu te + value + q ualifier + p m o ntolog y ter m : Ph enotyp e: (w ith asl2 ) ad u lt | v iab ility | v iab le | re cessive Ph enotyp e: (w ith asl3 ) ad u lt | v iability | vi ab le | recessive Ph enotyp e: ad u lt | fe mal e_fer tility | fem ale_ster ile | re cessive OR Ph enotyp e: re p ro d u ct ion | fema le_ fer tility | f em ale_ster ile | re cessive Ph enotyp e: ad u lt | m ale_fer tility | m ale_ste rile | rece ssive OR Ph enotyp e: re p ro d u ct ion | mal e_fer tility | ma le_ster ile | re cessive Ph enotyp e: o nion stage sper m atid & Nebe nk ern | size | v alu e\ :v ari able??? | re cessiv e Ph enotyp e: o nion stage sper m atid & nu cleu s | size | v alu e\:v ar iable??? | recessive Ph enotyp e: (w ith asl2) sper m atocyte & as ter | q u antitative | ab sen t | re cessive Ph enotyp e: (w ith asl3) sper m atocyte & as ter | q u antitative | ab sen t | re cessive Ph enotyp e: cen triole & sp er mat ocyte | q ua litative | no rma l | re cessive Ph enotyp e: cen tro som e sep ara tion | p ro cess | v alu e\ :ab norm al??? | re cessive Ph enotyp e: meiotic m etap has e I | re lative_sp eed | slow | re cessive
Cold Harboreed | slow | re cessive Ph enotyp e: meiotic anap hase I | Spring re lative_sp Phenotype Ontology Meeting
Another example
Allele combinations: as in asl1: Phenotype manifest in: (with asl2) spermatocyte & aster New system would be Phenotype: (with asl2) spermatocyte & aster | quantitative | absent
again - better were quantitative attribute implicit and unstated
Tricky to express
Free text things:
asl1 some nebenkern are associated with two centrioles instead of one as in wild-type
abnormal relationship between two observables
Bsb2 The laterals split near the distal tip as they elongate and at later stages they appear to be split over more of their length
observables showing progressive defect
Caa1DAR66 A few homozygotes exhibit neurons in the longitudinal tracts that appear to stall at some of the commissures, forming nodular growths
behaviour of one observable in relation to another forming nodular growth?
Equivalent alternatives:
motor_neuron ; CL:0000100 motor neuron ; FBbt:00005123
Structural issue:
Sense of compound observable/attribute combination: Observation: phenotype is in dorsal epithelium that makes the embryonic head
but combined (better) Phenotype: morphogenesis of embryonic epithelium & embryonic head epidermis | process | abnormal
issue - attribute meaningful for one but not other observable - different kind of &
Curation issues:
1: Need tools browser where only relevant values for specific attribute are presented statement builder to assemble compound phenotype terms sequentially from vocabs. 2: Redundancy solver - would certain combinations be disallowed in statement builder?
The Answers:
1: Can the Phenotype Ontology represent all the controlled data that FlyBase allele records include? - potentially yes 2: Can the Phenotype Ontology reduce the amount of free text information in FlyBase allele records? -yes, but probably not eliminate it 3: Is the proposed system efficient enough for curators for production database use? - no 4: Is the end product of this type of curation useful to biologists? - in searches yes though redundancy needs resolution, - for browsing? have found users to be tolerant