!!!!!!!!!!!
! generic !
!!!!!!!!!!!

[property]
id: successor_to
relationship: is_a variation_of

[term]
id: analysis_program
property: has_version string
property: has_vendor_impl vendor_impl
property: developed_by
property: has_sensitivity scale_val
property: has_selectivity scale_val
property: variation_of analysis_program

[term]
id: protocol
property: has_program analysis_program *
definition: a computable description of how to run a set of analyses

[term]
id: sequence_analysis_program
relationship: is_a analysis_program
property: has_query_sequence SO:so
property: has_query_sequence_source string

[term]
id: structure_prediction_program
relationship: is_a sequence_analysis_program

[term]
id: secondary_structure_prediction_program
relationship: is_a structure_prediction_program

[term]
id: rna_structure_prediction_program
relationship: is_a structure_prediction_program

[term]
id: na_sequence_analysis_program
relationship: is_a sequence_analysis_program
relationship: has_query_sequence SO:na

[term]
id: dna_sequence_analysis_program
relationship: is_a na_sequence_analysis_program

[term]
id: rna_sequence_analysis_program
relationship: is_a na_sequence_analysis_program
relationship: has_query_sequence SO:rna

[term]
id: transcribed_na_sequence_analysis_program
relationship: is_a na_sequence_analysis_program

[term]
id: aa_sequence_analysis_program
relationship: is_a sequence_analysis_program

[term]
id: nucleotide_motif_detection_program
relationship: is_a motif_detection_program
relationship: input_sequence_type SO:nucleotide

[term]
id: prediction_program
relationship: is_a sequence_analysis_program
property: predicts_type SO:so
property: model_source source
property: model_source_file source_file

!!!!!!!!!!!!!!
! prediction !
!!!!!!!!!!!!!!

! diff btwn motif and prediction??

[term]
id: protein_motif_detection_program
relationship: is_a prediction_program
relationship: predicts_type SO:protein_motif

[term]
id: interproscan
relationship: is_a protein_motif_detection_program
relationship: is_a protocol
relationship: has_program prints
relationship: has_program pfam

[term]
id: pfam
relationship: is_a protein_motif_detection_program

[term]
id: part_of_gene
relationship: part_of SO:gene

[term]
id: gene_prediction_program
relationship: is_a prediction_program
relationship: predicts_type part_of_gene

[term]
id: noncoding_gene_prediction_program
relationship: is_a gene_prediction_program
relationship: predicts_type SO:noncoding_transcript

[term]
id: trnascan-se
relationship: is_a noncoding_gene_prediction_program
relationship: predicts_type SO:tRNA

[term]
id: protein_coding_gene_prediction_program
relationship: is_a gene_prediction_program
relationship: predicts_type SO:CDS

[term]
id: fgenesh
relationship: is_a protein_coding_gene_prediction_program
relationship: predicts_type SO:CDS

[term]
id: fgenesh++
relationship: successor_to fgenesh

[term]
id: geneid
relationship: is_a protein_coding_gene_prediction_program
relationship: predicts_type SO:CDS

[term]
id: genewise
relationship: is_a protein_coding_gene_prediction_program
relationship: predicts_type SO:CDS

[term]
id: genscan
relationship: is_a protein_coding_gene_prediction_program
relationship: predicts_type SO:CDS
relationship: has_sensitivity high
relationship: has_selectivity low

[term]
id: genie
relationship: is_a protein_coding_gene_prediction_program
relationship: predicts_type SO:CDS
relationship: has_sensitivity low
relationship: has_selectivity high

[term]
id: combined_prediction_pairwise_alignment_program
relationship: is_a prediction_program
relationship: is_a pairwise_alignment_program

[term]
id: genie-EST
relationship: is_a combined_prediction_pairwise_alignment_program
relationship: is_a genie

[term]
id: twinscan
relationship: is_a combined_prediction_pairwise_alignment_program
relationship: predicts_type SO:mRNA

!!!!!!!!!!!!!
! alignment !
!!!!!!!!!!!!!

[term]
id: sequence_alignment_program
relationship: is_a sequence_analysis_program

[term]
id: structural_sequence_alignment_program
relationship: is_a sequence_alignment_program
definition: aligns using both primary and secondary structure

[term]
id: multiple_sequence_alignment_program
relationship: is_a sequence_alignment_program

[term]
id: tcoffee
relationship: is_a multiple_sequence_alignment_program

[term]
id: clustalw
relationship: is_a multiple_sequence_alignment_program

[term]
id: pairwise_sequence_alignment_program
relationship: is_a sequence_alignment_program

[term]
id: exonerate
relationship: is_a pairwise_sequence_alignment_program

[term]
id: sim4
relationship: is_a pairwise_sequence_alignment_program
relationship: seq_type genome_to_expressed

[term]
id: blast
relationship: is_a pairwise_sequence_alignment_program

[term]
id: blastn
cross_product: blast (seq_type nucleotide_to_nucleotide)

[term]
id: blastp
cross_product: blast (seq_type protein_to_protein)

[term]
id: blastx
cross_product: blast (seq_type nucelotide_to_protein)

[term]
id: tblastx
cross_product: blast (seq_type translated_nucleotide_to_nucleotide)

[term]
id: tblastn
cross_product: blast (seq_type protein_to_nucleotide)

[term]
id: seq_type
property: has_query_seq_type
property: has_subject_seq_type

[term]
id: nucleotide_seq_input
relationship: is_a seq_type
relationship: has_query_seq_type SO:nucleotide

[term]
id: protein_seq_input
relationship: is_a seq_type
relationship: has_query_seq_type SO:protein

[term]
id: nucelotide_to_protein
cross_product: nucleotide_seq_input (has_subject_seq_type SO:protein)

!!!!!!!!!!!!!!!!
! vendor_impl  !
!!!!!!!!!!!!!!!!

[term]
id: vendor_impl

[term]
id: ncbi
relationship: is_a vendor_impl

[term]
id: wu
relationship: is_a vendor_impl


!!!!!!!!!!!
! output  !
!!!!!!!!!!!

[term]
id: program_output
property: has_unit score_unit
property: has_program analysis_program

[term]
id: blast_score
cross_product: program_output (has_program blast)

! what about normalized!!!???
[term]
id: blast_bitscore
cross_product: blast_score (has_unit bit)

[term]
id: blast_natscore
cross_product: blast_score (has_unit nat)

[term]
id: score_unit

[term]
id: nat
relationship: is_a score_unit

[term]
id: bit
relationship: is_a score_unit
definition:

[term]
id: p_value
relationship: is_a program_output
definition: probability

[term]
id: e_value
relationship: is_a program_output
definition: expectation

[term]
id: conversion_formula
property: has_equation string
property: has_input value
property: has_output value

[term]
id: conversion_e_to_p
relationship: is_a conversion_formula
relationship: has_input e_value
relationship: has_output p_value
relationship: has_equation $input=$output blah blah... 

[term]
id: parameter
property: has_program analysis_program

!!!!!!!!!!!!!!!!!!!!
! program params   !
!!!!!!!!!!!!!!!!!!!!

[term]
id: program_parameter
relationship: is_a parameter

[term]
id: relative_entropy
relationship: is_a program_parameter

!!!!!!!!!!!
! input   !
!!!!!!!!!!!

[term]
id: input_parameter
relationship: is_a parameter
property: cmd_line_switch

[term]
id: scoring_matrix
relationship: is_a input_parameter

[term]
id: pam
relationship: is_a scoring_matrix
property: pam_num int

[term]
id: pam250
cross_product: pam (pam_num 250)

[term]
id: blosum
relationship: is_a scoring_matrix
property: blosum_num int

[term]
id: subject_sequence_source
relationship: is_a input_parameter

[term]
id: single_subject_sequence_source
relationship: is_a subject_sequence_source

[term]
id: multiple_subject_sequence_source
relationship: is_a subject_sequence_source

[term]
id: query_sequence_source
relationship: is_a input_parameter

!!!!!!!!!
[term]
id: command_line_fmt
property: has_program
property: fmt_str

[term]
id: ncbi_blast_command_line_fmt
cross_product: command_line_fmt (has_program ncbi_blast)
relationship: fmt_str 'blastall -p %has_program% -i ...'

[term]
id: program_installation
property: has_program analysis_program
property: has_site string
property: has_path string
property: has_installation_date

[term]
id: program_run
property: has_program analysis_program

[term]
id: foo

[instance]
class: query_sequence_source
propval: has_program blast
propval: cmd_line_switch -i

!!!!!!! END !!!!!!!!
