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Updated my base version of the project #3

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1c66448
Initial commit with the code prepared to execute queries against janu…
May 31, 2021
2c9aba9
Merge branch 'master' of https://github.com/Rothamsted/graphdb-benchm…
Jun 15, 2021
121cf3f
Including the gremlin connector and updating the neo4j queries
Jun 15, 2021
d6e2025
Preparing the gremlin tests, new branch only for java 1.8
cbobed Jun 15, 2021
bbdeb8f
Readme Update
cbobed Jun 15, 2021
56836dd
Start polishing and testing the queries in gremlin
cbobed Jun 15, 2021
2161d65
Before changing to master - new exec
cbobed Jul 5, 2021
36fe642
Removed in this version the Cypher evaluator due to compatibility
Oct 5, 2021
f3cccf1
Added some changes via the git command line
cbobed Oct 5, 2021
3b2e36c
Added the gremlin connector and updating the ne4ojqueries
Oct 5, 2021
2cb6823
Updating gremlin queries
Nov 26, 2021
5a201f9
Added cleaned versions of the csvs
Nov 26, 2021
eb58bea
Updated all the information for running the experiments
Nov 29, 2021
6aa457a
Strong rewriting effort in the gremlin queries 18/21
cbobed Dec 3, 2021
5d1ea6c
some additions to 190,200,210 in gremlin
cbobed Dec 12, 2021
c493d64
final version of the gremlin queries to be executed
cbobed Feb 14, 2022
37d6ef1
added the gremlin queries and the gremlin profiler
cbobed Feb 16, 2022
466c76f
Added 6 new queries coding semantic motifs
cbobed Feb 19, 2022
235d40c
Added the gremlin queries
cbobed Feb 21, 2022
90a26e9
q!
cbobed Feb 21, 2022
094b6ab
Fixed one iri argument missing
cbobed Feb 21, 2022
71c0745
Added the .csv files with the gene IRIs to master branch
cbobed Feb 21, 2022
6bafa9d
added the SPARQL queries for the semantic motifs
cbobed Feb 21, 2022
5abdfed
Added all the queries and csv needed for the cleaned experiments
cbobed Feb 22, 2022
4f4e65e
update to latest execution configuration
cbobed Feb 23, 2022
428fb29
latest configurations and querysets for all the executions
cbobed Feb 23, 2022
a612ee8
Latest changes to gremlin branch
cbobed Apr 2, 2023
5234b05
Merge branch 'Java1.8-Compatible'
cbobed Apr 2, 2023
d95e4e1
updated gremlin and groovy scripts
cbobed May 5, 2023
bb3f5cc
cleaned the gremlin dir with the queries, added janusgraphGroovyScripts
cbobed May 5, 2023
2609b68
Merge branch 'Java1.8-Compatible'
cbobed May 5, 2023
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20 changes: 15 additions & 5 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,5 +1,15 @@
.project
.settings/
target/
.classpath
.DS_Store
<<<<<<< HEAD
.project
.settings/
target/
.classpath
.DS_Store
/bin/
=======
.project
.settings/
target/
.classpath
.DS_Store
/bin/
>>>>>>> refs/heads/Java1.8-Compatible
156 changes: 156 additions & 0 deletions 0020_cntType.csv
Original file line number Diff line number Diff line change
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label
Treatment
Timepoint
Taxon
SequenceFeature
Sequence
PublicationList
Publication
ProcessSequence
PWM
OntologyTerms
Localizable
Interaction
HierarchyNode
Group
ExpressionAffector
Experiment
Annotation
ProtFam
MicroArrayExperiment
Disease
KO
PhysInt
GenInt
Space
Process
Participant
TO
PlantOntologyTerms
MeshTerm
MeSH
GeneOntologyTerms
CHEM
AHDPO
Path
NASEQ
AminoacidSequence
PolypeptideFeature
NucleotideFeature
Organism
Plant_Hormone
Cultivar
At_Mutant
TRRSubFeature
TRR
TFBS
SubtelomereSubFeature
Retrotransposon
Repeat
QTL
Pseudogene
Operon
ORF
NonTranscribedRegion
NcRNAGene
MultiGeneLocus
MatingLocusSubFeature
MatingLocus
GeneCassette
Gene
FeatureContainer
CentromereSubFeature
Centromere
CDS
ARSCons
ARS
Protein3DStructure
ProtDomain
TARGETSEQ
EST
SignallingPathway
MetabolicPathway
MolecularFunction
MolFunc
CellularComponent
CelComp
BiologicalProcess
BioProc
MeshSupplementalRecord
MeshSubstance
MeshSemanticType
MeshQualifier
MeshPharmacologicalAction
MeshDescriptor
MeshConcept
PO_PlantStructure
PO_GrowthStage
POTempStage
GRO
EC
MoleculeComplex
Molecule
MolCmplx
Transport
Reaction
Tissue
Environment
GISR
GISL
GISHI
GISGD
GIPS
GIPE
GIDR
GIDL
GIDGD
KOPR
KOGE
KOEN
Protein
InfoPolymer
Compound
Comp
ECorg
CDEIII
CDEII
CDEI
Scaffold
Chromosome
Z2Region
Z1Region
YRegion
XRegion
WRegion
TRNAGene
SNRNAGene
SNORNAGene
RRNAGene
STR
STBS
YPrime
XCore
TelomericRepeat
LTR
Transporter
TF
StrucProt
ProteinComplex
Protcmplx
Enzyme
Metabolite
Drug
Polypeptide
Polynucleotide
SF
RNA
DNA
sDNA
dDNA
ncRNA
MRNA
TRNA
SNRNA
SNORNA
SIRNA
RRNA
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