The JLW RDF vocabulary
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The JLW RDF vocabulary

This version:
https://www.sinergiawolfender.org/jlw/ontology_version/0.1.0
Revision:
0.1.0
Authors:
Marco Pagni, https://www.sib.swiss✉
Contributors:
Arnaud Gaudry, https://www.unige.ch✉
Florence Mehl, https://www.sib.swiss✉
Frédéric Burdet, https://www.sib.swiss✉
License:
https://creativecommons.org/licenses/by-nc-sa/4.0/
Visualization:
Visualize with WebVowl
Cite as:
Marco Pagni. The JLW RDF vocabulary. Revision: 0.1.0. Retrieved from: https://www.sinergiawolfender.org/jlw/ontology_version/0.1.0
Provenance of this page
Ontology Specification Draft

Abstract

This is a placeholder text for the abstract. The abstract should contain a couple of sentences summarizing the ontology and its purpose.

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

The JLW RDF vocabulary: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Named Individuals

The JLW RDF vocabulary: Description back to ToC

The RDF vocabulary describing concepts defined in the JLW dataset

Cross-reference for The JLW RDF vocabulary classes, object properties and data properties back to ToC

This section provides details for each class and property defined by The JLW RDF vocabulary.

Classes

A MZMine featurec back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/MZmineFeature

A spectral feature aligned by MZMine
is in domain of
has MZmine M/Z dp, has MZmine M/Z dp

A MZMine peakc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/MZMinePeak

A chromatogram peak after alignment by MZMine
is in range of
has MZMine strong feature op

Assay batch of resultsc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/AssayBatch

A collection of analyses acquired at the same time and at the same place under the same protocol. It might also be called an analytical batch.
has super-classes
/ Activity c, Collection c
is in domain of
article used by assay batch op, has operator op, protocol used by assay batch op
is in range of
belongs to an assay batch op
has members
Analogs Hits HDPBL collection ni, Analogs Hits Wolfrum collection ni, CT lab bio assay RSV Celastraceae ni, CT lab bio assay RSV PF1600 ni, CT lab bio assay RSV Taxodiverse ni, CW assay batch JUN2022 ni, CW assay batch MAY2023 ni, Celastraceae collection ni, Chemodiverse collection ni, Combretaceae collection ni, Expert collection ni, INVENTA aligned analysis results ni, INVENTA alignedanalysis results ni, INVENTA unaligned analysis results ni, INVENTA unaligned analysis results ni, MEMO analysis results ni, MZMINE analysis results ni, Olivier Xtra collection ni, PF tubes collection ni, PF200 collection ni, Smart collection ni, SwissTPH assay batch ni, TS lab bio assay APR 2023 ni, TS lab bio assay DEC 2022 ni, TS lab bio assay JAN 2024 ni, TS lab bio assay JUN 2023 ni, TS lab bio assay MAR 2023 ni, TS lab bio assay MAY 2022 ni, TS lab bio assay MAY 2023 ni, TS lab bio assay MAY 2024 ni, TS lab bio assay SEP 2023 ni, Taxodiverse collection ni, VGF extra plates collection ni, VK lab bio assay Wnt 1600 MAR 2020 ni, VK lab bio assay Wnt Celastraceae JAN 2020 ni, Validated Hits TS collection ni, Validation List TS collection ni

Assay result from CW labc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/CWAssayResult

Assay result from CW lab.
has super-classes
Assay result c
is in domain of
has LD area dp, has LD intensity dp, has PI staining dp, has autophagy dp, has cell number dp, has microscopic observation dp
is in range of
has CW bio assay result op

Assay result from MEMO protocolc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/MEMOAssayResult

Assay result from MEMO protocol.
has super-classes
Assay result c

Chemical compoundc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/ChemicalEntity

A pure chemical substance consisting of one or more different chemical elements
is in domain of
has GNPS Spectrum dp, has InChI dp, has InChIKey dp, has WD chem xref ap, has isomeric SMILES dp
is in range of
Has chemical entity op, LOTUS reports chemical op

Collection of PF codesc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/PFCodeCollection

A set of PF codes that were grouped together because they participate to the same analysis.
Example
https://www.sinergiawolfender.org/jlw/chemo_diverse_PFcode_collection
has super-classes
Collection c
is in range of
is part of PF code collection op

Cross referencec back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/XRef

A cross reference that point to an external resource
has sub-classes
Doc X Ref c, Img X Ref c

Doc X Refc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/DocXRef

A link to a browsable document on an external server (disjoint from jlw:IdXRef and jlw:ImgXRef)
has super-classes
Cross reference c
has sub-classes
OTT XRef c

helper image xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/SinwolfImgXRef

An image from www.singergiawolfender.org, directly or as a proxy
has super-classes
Img X Ref c

Img X Refc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/ImgXRef

A link to an image on an external server
has super-classes
Cross reference c
has sub-classes
USI image xref c, W D Img X Ref c, helper image xref c

Lab controlc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/LabControl

A physical sample used as a blank or QC standard in JLW
has super-classes
Lab sample c
has members
Lab control 1 ni, Lab control 2 ni

Lab extractc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/LabExtract

A Physical sample resulting from an extraction procedure
has super-classes
Lab sample c
is in domain of
has purified compound op, is part of experiment op, is part of selection round dp

Lab fractionc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/LabFraction

A physical sample resulting from an fractionation procedure
has super-classes
Lab sample c

Lab purified compoundc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/LabPurifiedCompound

Isolated from one or more samples
has super-classes
Lab sample c
is in range of
has purified compound op

LOTUS entryc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/LotusEntry

An entry with organism-chemical-citation from LOTUS
is in domain of
LOTUS reports chemical op, LOTUS reports citation op, LOTUS reports taxon op

MZMine chromatogramc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/MZmineChromatogram

A chromatogram after alignment by MZMine
is in domain of
has MZMine strong feature op, has MZMine strong feature op, has MZMine weak feature op
is in range of
has MZmine chromatogram op

OTT XRefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/OTTDocXRef

A cross reference to an Open Tree of Life identifier
has super-classes
Doc X Ref c

PF codec back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/PFCode

An entry code of the Pierre Fabre (PF) phytothèque. It corresponds to a single batch of plant collection. Different codes may refer to the same plant part and the same species, but in different batches i.e. different collection events.
Example
https://www.sinergiawolfender.org/jlw/V100042
has super-classes
Lab sample c
is in domain of
has broad taxon op, has exact taxon op, has narrow taxon op, has taxon op, is from plant part op, is part of PF code collection op

Placeholder taxon without OTT xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/UnknownTaxon

has super-classes
Taxon c

Plant partc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/PlantPart

A plant part, adapted from the original nomenclature of the Pierre Fabre phytothèque. See jlw:PlantPartScheme for more details
is in domain of
has rank dp, is part of plant part op
is in range of
is from plant part op, is part of plant part op

Protocol used in sinergiawolfenderc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/Protocol

Protocol used in sinergiawolfender
has super-classes
/ Entity c
is in domain of
protocol or article written by operator op
is in range of
protocol used by assay batch op
has members
Protocol for CW assays ni, Screening protocol ni, T S thesis J Nitschke ni, TPH protocol ni

Scientific paper used as a referencec back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/Article

Scientific paper used as a reference
has super-classes
/ Entity c
is in domain of
protocol or article written by operator op
is in range of
article used by assay batch op
has members
10.3389/fntpr.2023.1279761 ni, Paper results Soldati ni, doi.org/10.26434/chemrxiv-2023-sljbt ni, doi.org/10.3389/fmicb.2020.00266 ni, doi.org/10.3389/fmolb.2022.1028334 ni, doi.org/10.3389/fonc.2020.602817 ni, doi:10.3389/fbinf.2022.842964 ni

Taxonc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/Taxon

This is a taxon in a simplified taxonomy derived from Open Tree of Life (OTT) 3.3, with a few modifications. This 'local' taxonomy is a balanced tree and therefore contains a few additionnal (i.e. 'unknown') nodes for the sake of balancing lineages. All PF codes are all placed at the 'species' rank. This also has required to remap some infra-specific assignment to the species rank. In addition a few 'Genus sp.' nodes were created for PF codes originally assignement at the genus rank
has sub-classes
Placeholder taxon without OTT xref c, Taxon with an OTT xref c
is in domain of
has parent taxon op, has taxo rank dp
is in range of
has broad taxon op, has exact taxon op, has narrow taxon op, has parent taxon op, has taxon op

Taxon with an OTT xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/OttTaxon

has super-classes
Taxon c
is in domain of
has wikidata taxo xref op
is in range of
LOTUS reports taxon op

USI image xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/USIImgXRef

An image from metabolomics-usi.ucsd.edu
has super-classes
Img X Ref c

W D Img X Refc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/WDImgXRef

An image from www.wikidata.org
has super-classes
Img X Ref c

WD citation xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/WikidataCitationXRef

A cross reference to a citation in wikidata
has super-classes
Wikidata X Ref c
is in range of
LOTUS reports citation op

WD taxo xrefc back to ToC or Class ToC

IRI: https://www.sinergiawolfender.org/jlw/WikidataTaxoXRef

A cross reference to a taxon in wikidata
has super-classes
Wikidata X Ref c
is in range of
has wikidata taxo xref op

Object Properties

has broad taxonop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_broad_taxon

has super-properties
has taxon op
has domain
PF code c
has range
Taxon c
is also defined as
annotation property

Has chemical entityop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_chemical_entity

Physical chemical coming from a fraction
has domain
Resource c
Lab sample c
has range
Chemical compound c

has chemo assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_chemo_assay_result

has super-properties
has assay result op
has domain
Lab sample c
has range
Assay result c

has CT bio assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_CT_bio_assay_result

has super-properties
has bio assay result op
has domain
Lab sample c
has range
O H Assay Result c

has CW bio assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_CW_bio_assay_result

has super-properties
has bio assay result op
has domain
Lab sample c
has range
Assay result from CW lab c

has exact taxonop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_exact_taxon

has super-properties
has taxon op
has domain
PF code c
has range
Taxon c
is also defined as
annotation property

has in-silico assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_insilico_assay_result

has super-properties
has assay result op
has sub-properties
has INVENTA in-silico assay result op
has domain
Lab sample c
has range
Assay result c

has INVENTA in-silico assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_INVENTA_insilico_assay_result

has super-properties
has in-silico assay result op
has domain
Lab sample c
has range
Assay result from INVENTA protocol c

has lab processop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_lab_process

has domain
Lab sample c
has range
Lab sample c
is also defined as
named individual

has MZMine strong featureop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZMine_feature

has domain
M Zmine Peak c
has range
M Z Mine Feature c

has MZMine strong featureop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZmine_peak

has domain
MZMine chromatogram c
has range
A MZMine peak c

has MZMine weak featureop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZmine_feature_WEAK

Strong and weak sets of features are disjoint
has domain
MZMine chromatogram c
has range
M Z Mine Feature c

has narrow taxonop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_narrow_taxon

has super-properties
has taxon op
has domain
PF code c
has range
Taxon c
is also defined as
annotation property

has parent taxonop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_parent_taxon

has domain
Taxon c
has range
Taxon c
is also defined as
annotation property

has purified compoundop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_purified_compound

has purified compound
has domain
Lab extract c
has range
Lab purified compound c

has purified sampleop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_purified_sample

has domain
Lab sample c
has range
Lab sample c
is also defined as
annotation property

has taxonop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_taxon

has sub-properties
has broad taxon op, has exact taxon op, has narrow taxon op
has domain
PF code c
has range
Taxon c

has TPH bio assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_SwissTPH_bioassay_result

has super-properties
has bio assay result op
has domain
Lab sample c
has range
Assay result from TPH lab c

has TS bio assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TS_bio_assay_result

has super-properties
has bio assay result op
has domain
Lab sample c
has range
Assay result from TS lab c

has VK bio assay resultop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_VK_bio_assay_result

has super-properties
has bio assay result op
has domain
Lab sample c
has range
Assay result from VK lab c

has wikidata taxo xrefop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_wikidata_taxo_xref

has domain
Taxon with an OTT xref c
has range
WD taxo xref c
is also defined as
named individual

is from plant partop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/is_from_plant_part

has domain
PF code c
has range
Plant part c

is part of experimentop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/is_part_of_experiment

has domain
Lab extract c
has range
Sample Collection c
is also defined as
annotation property

is part of PF code collectionop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/is_part_of_PFcode_collection

has domain
PF code c
has range
Collection of PF codes c
is also defined as
annotation property

is part of plant partop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/is_part_of

has domain
Plant part c
has range
Plant part c
is also defined as
annotation property

protocol or article written by operatorop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_author

has domain
Scientific paper used as a reference c
Protocol used in sinergiawolfender c
has range
Person c
is also defined as
annotation property

protocol used by assay batchop back to ToC or Object Property ToC

IRI: https://www.sinergiawolfender.org/jlw/usedProtocol

has domain
Assay batch of results c
has range
Protocol used in sinergiawolfender c
is also defined as
annotation property

Data Properties

has a Wnt Cytotoxicitydp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_cytotoxic_effect

MTT IC50 of BT-20 TNBC cell viability
has super-properties
has a Wnt Cytotoxicity dp
has sub-properties
has a Wnt Cytotoxicity dp
has domain
Assay result from VK lab c
has range
double

has GNPS Spectrumdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_GNPS_Spectrum

has GNPS Spectrum
has domain
Chemical compound c
has range
string

has in cellulo_exp_iddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_in_cellulo_exp_id

has domain
Assay result from TS lab c
has range
string
is also defined as
named individual

has in vitro exp iddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_in_vitro_exp_id

has domain
Assay result from TS lab c
has range
string
is also defined as
named individual

has InChIdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_InChI

has standard InChI
has domain
Chemical compound c
has range
string

has InChIKeydp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_InChIKey

has standard InChI key
has domain
Chemical compound c
has range
string

has isomeric SMILESdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_SMILES_iso

has isomeric SMILES
has domain
Chemical compound c
has range
string

has lab book initalsdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/lab_book_initals

has domain
Lab sample c
has range
string
is also defined as
named individual

has MZmine M/Zdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZmine_MZ

has domain
A MZMine feature c
has range
double

has MZmine M/Zdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZmine_RT

has domain
A MZMine feature c
has range
double

has MZMine strong featuredp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_MZMine_area

has domain
M Zmine Peak c
has range
double

has process typedp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_process_type

has domain
Lab sample c
has range
string
is also defined as
named individual

has putative interpretationdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_putative_interpretation

has domain
Assay result from TS lab c
has range
string
is also defined as
named individual

has rankdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_rank

has domain
Plant part c
has range
string
is also defined as
named individual

has remaining growth dd in infectiondp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_dd_in_infection

has domain
Assay result from TS lab c
has range
double
is also defined as
annotation property, named individual

has remaining growth dd in infection sddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_dd_in_infection_sd

has domain
Assay result from TS lab c
has range
double
is also defined as
annotation property, named individual

has remaining growth mm in infectiondp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_infection

has domain
Assay result from TS lab c
has range
double
is also defined as
annotation property, named individual

has remaining growth mm in infection sddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_infection_sd

has domain
Assay result from TS lab c
has range
double
is also defined as
annotation property, named individual

has RSV Cytotoxicity on A549 cellsdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_RSV_cytotoxic_effect

Resazurine Percentage of cell viability in reference to the control on A549 cells, 50 ug ml extract
has super-properties
has RSV Inhibitory effect dp
has domain
Assay result from CT lab c
has range
double

has RSV Cytotoxicity on A549 cellsdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_RSV_cytotoxic_effect_cat

has domain
Assay result from CT lab c
has range
string
is also defined as
annotation property

has RSV Inhibitory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_RSV_effect

has sub-properties
has RSV Cytotoxicity on A549 cells dp
has domain
Assay result from CT lab c
has range
double
is also defined as
annotation property

has RSV Inhibitory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_RSV_effect_cat

has domain
Assay result from CT lab c
has range
string
is also defined as
annotation property

has solventdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_solvent

has domain
Lab sample c
has range
string
is also defined as
named individual

has taxo rankdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_taxo_rank

has domain
Taxon c
has range
string
is also defined as
annotation property, named individual

has TPH L donovani 10ug mldp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_L_donovani_10ug_ml

has domain
Assay result from TPH lab c
has range
double
is also defined as
named individual

has tube quantitydp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_tube_quantity

has domain
Lab sample c
has range
double
is also defined as
named individual

has Wnt Activatory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_activatory_effect

IC50 Wnt activation on BT-20 TNBC
has super-properties
has Wnt Activatory effect dp
has domain
Assay result from VK lab c
has range
double

has Wnt Activatory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_effect

has sub-properties
has Wnt Activatory effect dp, has Wnt Inhibitory effect dp
has domain
Assay result from VK lab c
has range
double
is also defined as
annotation property

has Wnt Activatory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_effect_cat

has domain
Assay result from VK lab c
has range
string
is also defined as
annotation property

has Wnt Inhibitory downstream-regulated effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_downstream_inhibitory_effect

IC50 Wnt downstream inhibition on BT-20 TNBC
has super-properties
has Wnt Inhibitory effect dp
has domain
Assay result from VK lab c
has range
double

has Wnt Inhibitory effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_inhibitory_effect

IC50 Wnt inhibition on BT-20 TNBC
has super-properties
has Wnt Activatory effect dp
has sub-properties
has Wnt Inhibitory downstream-regulated effect dp, has Wnt Inhibitory upstream-regulated effect dp
has domain
Assay result from VK lab c
has range
double

has Wnt Inhibitory upstream-regulated effectdp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_Wnt_upstream_inhibitory_effect

IC50 Wnt upstream inhibition on BT-20 TNBC
has super-properties
has Wnt Inhibitory effect dp
has domain
Assay result from VK lab c
has range
double

is part of selection rounddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/is_part_of_selection_round

has domain
Lab extract c
has range
string
is also defined as
named individual

Obtained quantitydp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_obtained_quantity

Obtained quantity [g]
has domain
Lab sample c
has range
double

Process yielddp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_process_yield

Process yield [%]
has domain
Lab sample c
has range
double

Stock quantitydp back to ToC or Data Property ToC

IRI: https://www.sinergiawolfender.org/jlw/has_stock_quantity

has domain
Lab sample c
has range
double
is also defined as
named individual

Named Individuals

10.3389/fntpr.2023.1279761ni back to ToC or Named Individual ToC

IRI: https://www.frontiersin.org/articles/10.3389/fntpr.2023.1279761

Targeted isolation of natural analogs of anti-mycobacterial hit compounds based on the metabolite profiling of a large collection of plant extracts
belongs to
Scientific paper used as a reference c

1600 PFcodesni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/PFCode_1600_PFcode_collection

The collection of 1600 PF codes, which were originally screened and described in https://doi.org/10.1093/gigascience/giac124
belongs to
P Fcode Collection c
has facts
has pmid xref ap 36649739 ep

A simplified but balanced taxonomyni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/SimplifiedTaxonomyScheme

A simplified taxonomy derived from Open Tree of Life ver. 3.3. It is a balanced tree (all branches have the same length) and therefore contains a few placeholder nodes for the sake of balancing lineages. PF codes are now linked with nodes at the species rank. Some infra-specific assignment (e.g. cultivar) were remapped on the upper species. In addition, a few 'Genus sp.' nodes were created for PF codes originally assignement at the genus rank. When feasible link to wikidata taxonomy are also provided
belongs to
Concept Scheme c
has facts
has Top Concept ap taxon ott 805080 ep

All PF samplesni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/PFCodeFullCollection

The full collection of PF codes, most of them have not been screened to date.
belongs to
P Fcode Collection c

Analogs Hits HD-PBL PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/analogs_Hits_HD_PBL_PFcode_collection

7 plants that were selected on the basis of annotations matching structures of the 37 top Hit compounds in the HD-PBL List ( https://doi.org/10.3389/fmicb.2020.00266 ). One plant was extensively studied (V114260 – Cananga brandisiana – subterranean parts) and an article within the Sinergia is about to get published on this ( https://doi.org/10.3389/fntpr.2023.1279761 ).
belongs to
P Fcode Collection c

Analogs Hits Wolfrum PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/analogs_Hits_Wolfrum_PFcode_collection

4 plants that were selected on the basis of annotations matching structures of the 18 top Hit compounds in the Wolfrum Lab assays.
belongs to
P Fcode Collection c

belongs to an assay batchni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/in_assay_result_batch

belongs to
property c
is also defined as
annotation property, object property

Celastraceae PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Celastraceae_PFcode_collection

All the Celastraceae in the 17k samples, analyzed by Luis during his PhD for the developement of INVENTA. Collection described in https://doi.org/10.26434/chemrxiv-2023-93gm5
belongs to
P Fcode Collection c

Chemo-diverse PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/chemo_diverse_PFcode_collection

First selection of plant made by the SIB based on taxo/chemo-diversity (Genetic algorithm?). 23 Plants extracted directly (and only with Ethyle acetate)
belongs to
P Fcode Collection c
has facts
example ap "jlw:V112049"

Combretaceae PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Combretaceae_PFcode_collection

Selection of 38 Combretaceae plants within the whole Pierre Fabre Library. Based on previous knowledge of interesting anti-mycobacterial activity found in plants of this family.
belongs to
P Fcode Collection c

CT lab bio assay RSV PF1600ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_CT_RSV_PF1600

RSV Inhibitory bioactivity assay performed in Caroline Tapparel lab on a subset of the PF1600 collection (plates VGF150-VGF159), the TAXODIVERSE and CELASTRACEAE Collections, first run (2023)
belongs to
Assay batch of results c
has facts
has operator op Paola Haemmerli ni
download U R L ap https://www.sinergiawolfender.org/protected/jlw/data/VGF150_159_results_RSV.tsv
/generated At Time ap "2023-12"^^g Year Month

CW assay batch JUN2022ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_CW_JUN2022

Cell culture microscopy analysis performed in CW lab, first run (JUN2022)
belongs to
Assay batch of results c
has facts
has operator op Chunyan Wu ni
protocol used by assay batch op Protocol for CW assays ni
access U R L ap "sinergiawolfender/groups/wolfrum_lab_data"
/generated At Time ap "2022-06"^^g Year Month

CW assay batch MAY2023ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_CW_MAY2023

Cell culture microscopy analysis performed in CW lab, second run (MAY2023)
belongs to
Assay batch of results c
has facts
has operator op Chunyan Wu ni
protocol used by assay batch op Protocol for CW assays ni
access U R L ap "sinergiawolfender/groups/wolfrum_lab_data/MAY2023"
/generated At Time ap "2023-05"^^g Year Month

doi.org/10.26434/chemrxiv-2023-sljbtni back to ToC or Named Individual ToC

IRI: https://doi.org/10.26434/chemrxiv-2023-sljbt

A Sample-Centric and Knowledge-Driven Computational Framework for Natural Products Drug Discovery
belongs to
Scientific paper used as a reference c

doi.org/10.3389/fmicb.2020.00266ni back to ToC or Named Individual ToC

IRI: https://doi.org/10.3389/fmicb.2020.00266

Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models
belongs to
Scientific paper used as a reference c

doi.org/10.3389/fmolb.2022.1028334ni back to ToC or Named Individual ToC

IRI: https://doi.org/10.3389/fmolb.2022.1028334

Inventa: A computational tool to discover structural novelty in natural extracts libraries
belongs to
Scientific paper used as a reference c

doi.org/10.3389/fonc.2020.602817ni back to ToC or Named Individual ToC

IRI: https://doi.org/10.3389/fonc.2020.602817

Beyond TNBC: Repositioning of Clofazimine Against a Broad Range of Wnt-Dependent Cancers
belongs to
Scientific paper used as a reference c

doi:10.3389/fbinf.2022.842964ni back to ToC or Named Individual ToC

IRI: https://doi.org/10.3389/fbinf.2022.842964

MEMO: Mass Spectrometry-Based Sample Vectorization to Explore Chemodiverse Datasets
belongs to
Scientific paper used as a reference c

Expert PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/expert_PFcode_collection

Selection of 40 plants based on the best candidates in terms of Wolfrum Lab assays (LD, Autophagy, PI) as well as Inventa results. Homemade algorithm by LFX and OK in October 2021
belongs to
P Fcode Collection c

has in cellulo_exp_idni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_in_cellulo_exp_id

belongs to
property c
is also defined as
data property

has in vitro exp idni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_in_vitro_exp_id

belongs to
property c
is also defined as
data property

has INVENTA PS Priority scoreni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_INVENTA_Priority_Score_PS

belongs to
property c
is also defined as
annotation property, data property

has INVENTA reported compounds in familyni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_INVENTA_reported_comp_family

belongs to
property c
is also defined as
annotation property, data property

has INVENTA reported compounds in genusni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_INVENTA_reported_comp_genus

belongs to
property c
is also defined as
annotation property, data property

has INVENTA reported compounds in speciesni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_INVENTA_reported_comp_species

belongs to
property c
is also defined as
annotation property, data property

has lab book initalsni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/lab_book_initals

belongs to
property c
is also defined as
data property

has lab processni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_lab_process

belongs to
Lab process c
is also defined as
object property

has microscopic observationni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_microscopic_observation

belongs to
property c
is also defined as
annotation property, data property

has process typeni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_process_type

belongs to
property c
is also defined as
data property

has putative interpretationni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_putative_interpretation

belongs to
property c
is also defined as
data property

has rankni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_rank

belongs to
property c
is also defined as
data property

has remaining growth dd in infectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_dd_in_infection

belongs to
property c
is also defined as
annotation property, data property

has remaining growth dd in infection sdni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_dd_in_infection_sd

belongs to
property c
is also defined as
annotation property, data property

has remaining growth mm in brothni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_broth

belongs to
property c
is also defined as
annotation property, data property

has remaining growth mm in broth sdni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_broth_sd

belongs to
property c
is also defined as
annotation property, data property

has remaining growth mm in infectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_infection

belongs to
property c
is also defined as
annotation property, data property

has remaining growth mm in infection sdni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_remaining_growth_mm_in_infection_sd

belongs to
property c
is also defined as
annotation property, data property

has solventni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_solvent

belongs to
property c
is also defined as
data property

has TPH Cytotoxicity 10ug mlni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_Cytotoxicity_10ug_ml

belongs to
property c
is also defined as
annotation property, data property

has TPH L donovani 10ug mlni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_L_donovani_10ug_ml

belongs to
property c
is also defined as
data property

has TPH L donovani 2ug mlni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_L_donovani_2ug_ml

belongs to
property c
is also defined as
annotation property, data property

has TPH T b rhodesiense 10ug mlni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_T_b_rhodesiense_10ug_ml

belongs to
property c
is also defined as
annotation property, data property

has TPH T b rhodesiense 2ug mlni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_TPH_T_b_rhodesiense_2ug_ml

belongs to
property c
is also defined as
annotation property, data property

has tube quantityni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_tube_quantity

belongs to
property c
is also defined as
data property

has wikidata taxo xrefni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_wikidata_taxo_xref

belongs to
property c
is also defined as
object property

is part of selection roundni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/is_part_of_selection_round

belongs to
property c
is also defined as
data property

Jean-Luc Wolfenderni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Jean-Luc_Wolfender

belongs to
/ Person c
Person c
has facts
affiliation ap https://www.unige.ch ep
email ap mailto:Jean-Luc.Wolfender@unige.ch ep
identifier ap 0000 0002 0125 952 X ep
name ap "Jean-Luc Wolfender"

Lab control 1ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/lab_ctrl_1

A sample in well 01 used for a QC standard in JLW lab or for DMSO blank in CW lab
belongs to
Lab control c

Lab control 2ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/lab_ctrl_2

A sample in well 12 used for blank in JLW lab or for tamoxifen control in CW lab
belongs to
Lab control c

Louis-Félix Nothiasni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Louis-Felix_Nothias

belongs to
/ Person c
Person c
has facts
affiliation ap https://www.unige.ch ep
email ap mailto:Louis-Felix.Nothias@unige.ch ep
identifier ap 0000 0001 6711 6719 ep
name ap "Louis-Félix Nothias"

Luis-Manuel Quiros-Guerreroni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Luis-Manuel_Quiros-Guerrero

belongs to
/ Person c
Person c
has facts
affiliation ap https://www.unige.ch ep
email ap mailto:Luis.Guerrero@unige.ch ep
identifier ap 0000 0002 1630 8697 ep
name ap "Luis-Manuel Quiros-Guerrero"

MEMO analysis resultsni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_MEMO

MEMO analysis results for the same samples than in the original MEMO paper (see protocol).
belongs to
Assay batch of results c
has facts
has operator op Arnaud Gaudry ni
/generated ap doi:10.3389/fbinf.2022.842964 ni
/generated At Time ap "2022"^^g Year Month

MZMINE analysis resultsni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_MZMINE

MZMINE data mining analysis results
belongs to
Assay batch of results c
has facts
has operator op Pierre-Marie Allard ni
/generated ap giac124 ep
/generated At Time ap "202X"^^g Year Month

Paper results Soldatini back to ToC or Named Individual ToC

IRI: https://doi.org/paperResultsSoldati

Paper results Soldati
belongs to
Scientific paper used as a reference c

Pierre-Marie Allardni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/Pierre-Marie_Allard

belongs to
/ Person c
Person c
has facts
affiliation ap https://unifr.ch/ ep
email ap mailto:pierre-marie.allard@unifr.ch ep
identifier ap 0000 0003 3389 2191 ep
name ap "Pierre-Marie Allard"

Plant part schemeni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/PlantPartScheme

A hierachical organization of plant parts adapted from the nomenclature found in the Pierre Fabre phytothèque. It is designed to capture most of the original annotations in a not-too-big hierarchy. A few rarely used or ambiguous designations were not taken into account (they are still visible in the comments of PfCode entries). Nota Bene: this scheme includes both plant organs sensu stricto (e.g. 'leaf' or 'flower') and practical categories with no botanical meaning (e.g. 'woody stem')
belongs to
Concept Scheme c
has facts
has Top Concept ap whole plant ep

Screening protocolni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/TSProtocol_20230801

Lab operations for an infection and broth bioassay
belongs to
Protocol used in sinergiawolfender c
has facts
protocol or article written by operator op Jahn Nitschke ni
/generated At Time ap "2023-08-01"^^date

SMART PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/SMART_PFcode_collection

Selection made by the SIB, where 177 plants could be received from Pierre Fabre, were extracted (Hexane + Ethyle acetate + methanol extracts). Some Ceasalpiniaceae + Goniothalamus plants were ordered and worked alongside the SMART selection and were included in the workflow/plates that were sent for biology testing, despite not being part of the SMART selection (192 plants in total).
belongs to
P Fcode Collection c

Stock quantityni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/has_stock_quantity

belongs to
property c
is also defined as
data property

SwissTPH assay batchni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_SwissTPH

SwissTPH assay batch on ... as decribed in ...
belongs to
Assay batch of results c
has facts
protocol used by assay batch op 649ea085ba3e99daef499a00 ni
/generated At Time ap "2022"^^g Year Month

Taxodiverse PFcode collectionni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/taxodiverse_PFcode_collection

Selection made by the SIB, where we used extracts available in tubes at the Wolfender lab (without new extraction from the plants). This set was meant to maximise the taxonomical diversity of what can be found within the entire 15000+ Pierre Fabre Library, but also excluding (?) the 1600 set that was already used to generate the SMART Library. 192 out of 200 plants selected had corresponding extracts (8 were missing).
belongs to
P Fcode Collection c

VK lab bio assay Wnt 1600 MAR 2020ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_VK_Wnt_1600

Wnt-regulation bioactivity assay performed in Vladimir Katanaev lab on the PF1600 collection, first run (2020)
belongs to
Assay batch of results c
has facts
has operator op Alexey Koval ni
article used by assay batch op doi.org/10.3389/fonc.2020.602817 ni
download U R L ap https://www.sinergiawolfender.org/protected/jlw/data/PF1600_Wnt.csv
/generated At Time ap "2020-03"^^g Year Month

VK lab bio assay Wnt Celastraceae JAN 2020ni back to ToC or Named Individual ToC

IRI: https://www.sinergiawolfender.org/jlw/assay_batch_VK_Wnt_Celastraceae

Wnt-regulation bioactivity assay performed in Vladimir Katanaev lab on the Celastraceae collection, first run (2020)
belongs to
Assay batch of results c
has facts
has operator op Alexey Koval ni
article used by assay batch op doi.org/10.3389/fonc.2020.602817 ni
download U R L ap https://www.sinergiawolfender.org/protected/jlw/data/Celastraceae_wnt.tsv
/generated At Time ap "2020-01"^^g Year Month

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals
ep: External Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.