#NOTE: Generated with DIGITtally version: DT1 
#NOTE: Versions of included data: AegyptiAtlas-7th October 2022/FlyAtlas1-7th October 2022/FlyAtlas2-3rd March 2025/FlyBase-FB2025_01/FlyCellAtlas-7th August 2023/MozAtlas-7th October 2022/MozTubules-7th October 2022/SilkDB3-7th October 2022

Chosen sources:     FlyAtlas1,    FlyAtlas2,    FlyCellAtlas,    FlyBase,    DIOPT,    MozAtlas,    MozTubules,    AegyptiAtlas,    SilkDB,    

The global weights for these sources are:
FlyAtlas1:      1
FlyAtlas2:      1
FlyCellAtlas:      1
FlyBase:      1
DIOPT:      1
MozAtlas:      1
MozTubules:      1
AegyptiAtlas:      1
SilkDB:      1


Chosen scores:Enrichment,    Specificity,    Ubiquity,    Published Association,    Orthology,    Hsap,    Agam,    Aaeg,    Bmor,    

The global weights for these scoring metrics are:
Enrichment:      1
Specificity:      1
Ubiquity:      1
Published Association:      1
Orthology:      1
Hsap:      1
Agam:      1
Aaeg:      1
Bmor:      1



-----INDIVIDUAL SOURCE SETTINGS-----

FlyAtlas1 settings 

type_use_Adult:      True
type_obligatory_Adult:      True
type_use_Larval:      True
type_obligatory_Larval:      False
metricweight_Enrichment:      1
metricweight_Specificity:      1
metricthreshold_Enrichment:      2.5
Enrichment_additionalThreshold:      True
Enrichment_additionalThresholdvalue:      2.0
metricthreshold_Specificity:      1.0
Specificity_additionalThreshold:      False
Specificity_additionalThresholdvalue:      2.0
microarray_precenceThreshold:      3
permissive_tissues:      ['']
tissues:      ['Midgut', 'Hindgut', 'Malpighian tubule', 'Salivary gland']
permitted:      ['']


FlyAtlas2 settings 

type_use_Male:      True
type_obligatory_Male:      True
type_use_Female:      True
type_obligatory_Female:      True
type_use_Larval:      True
type_obligatory_Larval:      False
metricweight_Enrichment:      1
metricweight_Specificity:      1
metricthreshold_Enrichment:      2.5
Enrichment_additionalThreshold:      True
Enrichment_additionalThresholdvalue:      2.0
metricthreshold_Specificity:      1.0
Specificity_additionalThreshold:      False
Specificity_additionalThresholdvalue:      2.0
rnaseq_FPKMThreshold:      2
permissive_tissues:      ['19']
tissues:      ['Midgut', 'Hindgut', 'Malpighian Tubules', 'Salivary gland']
permitted:      ['Rectal pad']


FlyCellAtlas settings 

metricweight_Enrichment:      1
metricweight_Specificity:      1
metricweight_Ubiquity:      1
metricweight_CoExpression:      1
metricthreshold_Enrichment:      0.001
scRNA_UMIThreshold:      1
celltypes:      ['Malpighian tubule : Salivary gland', 'Malpighian tubule : Adult malpighian tubule stellate cell of main segment', 'Malpighian tubule : Adult malpighian tubule principal cell of lower segment', 'Malpighian tubule : Adult malpighian tubule principal cell of lower ureter', 'Malpighian tubule : Adult malpighian tubule principal cell of initial segment', 'Malpighian tubule : Principal cell*', 'Malpighian tubule : Adult malpighian tubule principal cell', 'Malpighian tubule : Adult malpighian tubule principal cell subtype', 'Malpighian tubule : Adult malpighian tubule bar-shaped cell of initial segment', 'Malpighian tubule : Adult midgut*', 'Malpighian tubule : Posterior midgut*', 'Malpighian tubule : Midgut', 'Malpighian tubule : Adult hindgut*', 'Malpighian tubule : Adult hindgut', 'Gut : Adult midgut-hindgut hybrid zone', 'Gut : Malpighian tubule', 'Gut : Enteroendocrine cell', 'Gut : Enterocyte-like', 'Gut : Adult differentiating enterocyte', 'Gut : Enteroblast', 'Gut : Midgut large flat cell', 'Gut : Enterocyte of posterior adult midgut epithelium', 'Gut : Enterocyte of anterior adult midgut epithelium', 'Gut : Adult midgut enterocyte', 'Gut : Copper cell', 'Gut : Adult pylorus']


FlyBase settings 

choice_UseAssociation:      True
choice_UsePhenotype:      True
metricweight_Association:      1
metricweight_Phenotype:      1
vocab:      ['Malpighian tubule', 'salivary gland', 'midgut', 'hindgut']


DIOPT settings 

choice_UseOrthoDetection:      True
choice_UseDiseaseAssociation:      True
metricweight_OrthoDetection:      1
metricweight_DiseaseAssociation:      1
DIOPT_orthoscoreThreshold:      3


MozAtlas settings 

type_use_Male:      True
type_use_Female:      True
metricweight_Enrichment:      1
metricweight_Specificity:      1
metricweight_Any:      1
metricthreshold_Enrichment:      2.5
metricthreshold_Specificity:      1.0
microarray_precenceThreshold:      3
tissues:      ['Salivary Gland', 'Midgut', 'Malpighian Tubule']


MozTubules settings 

type_use_Male:      True
type_use_Female:      True
type_use_Larval:      True
type_use_Adult:      True
metricthreshold_Enrichment:      2.5
moztubules_to_mozatlastissue:      1


AegyptiAtlas settings 

metricweight_Enrichment:      1
metricweight_Specificity:      1
metricweight_Any:      1
metricthreshold_Enrichment:      2.5
metricthreshold_Specificity:      1.0
rnaseq_FPKMThreshold:      2
tissues:      ['Malpighian Tubules', 'Malpighian Tubules', 'Anterior Midgut', 'Posterior Midgut', 'Hindgut']


SilkDB settings 

type_use_Larvae_4thInstar:      True
type_use_Larvae_4thMolt:      True
type_use_Larvae_5thInstar:      True
type_use_Larvae_Wandering:      True
type_use_Larvae_PrePupa:      True
type_use_Pupa:      True
type_use_Moth:      True
choice_UseAnyStage:      True
choice_UseAllStage:      True
metricweight_Enrichment:      1
metricweight_Specificity:      1
metricweight_Any:      1
metricthreshold_Enrichment:      2.5
metricthreshold_Specificity:      1.0
rnaseq_FPKMThreshold:      2
tissues:      ['Malpighian Tubule', 'Midgut']


