Discussion:Espace Interactions Arbres Microorganismes/Serveurs : Différence entre versions

Version actuelle datée du 21 novembre 2020 à 16:38

Sommaire

1 Protocole
2 Modèle de paramétrage

Protocole

définir la séquence d'appel (ci dessous)
générer le serveur sur machine développement
installer les pages wikis
installer les fichiers
mettre à jour l'en-tête et la page serveur
mettre à jour Modèle:Wicri Bois lien serveur

Modèle de paramétrage

Sur machine locale (mac)

cd $WICRI_ROOT/Bois/explor/Thaumatin.storage

NlmPubMedExplorCorpus  -d ThaumatinV1  \
          -q "thaumatin" -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration Thomatine"

NlmPubMedGetCorpusSize -q '"rust effector*"'

cd $WICRI_ROOT/Bois/explor/RustEffector.storage

NlmPubMedExplorCorpus  -d RustEffectorV1  \
          -q '"rust effector*"' -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les effecteurs de la rouille "

NlmPubMedGetCorpusSize -q phanerochaete

cd $WICRI_ROOT/Bois/explor/Phanerochaete.storage

NlmPubMedExplorCorpus  -d PhanerochaeteV1  \
          -q Phanerochaete -s 2000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur le phanerochaete"

NlmPubMedGetCorpusSize -q "white rot"

cd $WICRI_ROOT/Bois/explor/WhiteRot.storage

NlmPubMedExplorCorpus  -d WhiteRotV1  \
          -q "white rot" -s 4000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la pourriture ligneuse"

NlmPubMedGetCorpusSize -q willow

cd $WICRI_ROOT/Bois/explor/Willow.storage

NlmPubMedExplorCorpus  -d WillowV1  \
          -q willow -s 5000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur le saule"

Sur VM LorExplor

NlmPubMedGetCorpusSize -q "phytophthora effector"


mkdir $WICRI_ROOT/Bois/explor/PhytophthoraEffector.storage

cd $WICRI_ROOT/Bois/explor/PhytophthoraEffector.storage

NlmPubMedExplorCorpus  -d "PhytophthoraEffectorV1"  \
          -q "phytophthora effector" -s 5000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les effecteurs du phytophthora"

Retour machine locale

NlmPubMedGetCorpusSize -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'

7974

mkdir $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage

cd $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage

NlmPubMedExplorCorpus  -d RustFungiGenomicsV1   \
          -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'   -s 8000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la génomique des pucciniales"

NlmPubMedGetCorpusSize -d -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])'

1989

mkdir $WICRI_ROOT/Bois/explor/BiopestPeptid.storage

cd $WICRI_ROOT/Bois/explor//BiopestPeptid.storage

NlmPubMedExplorCorpus  -d BiopestPeptidV1  \
          -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])' -s 7000    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les peptides biopesticides"

NlmPubMedGetCorpusSize -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])'

6033

mkdir $WICRI_ROOT/Bois/explor/RapamycinFungus.storage

cd $WICRI_ROOT/Bois/explor/RapamycinFungus.storage

NlmPubMedExplorCorpus  -d RapamycinFungusV1  \
          -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])' -s 3500    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur la rapamycine et les champignons"

Volumétrie croissante

cas simple

NlmPubMedGetCorpusSize -q "wood degradation fungi"

mkdir $WICRI_ROOT/Bois/explor/WoodDegFungi.storage

cd $WICRI_ROOT/Bois/explor/WoodDegFungi.storage

NlmPubMedExplorCorpus  -d WoodDegFungiV1   \
          -q "wood degradation fungi" -s 250    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les champignons de dégradation du bois"

NlmPubMedGetCorpusSize -q "plant glutathione transferases "

mkdir $WICRI_ROOT/Bois/explor/PlantGlutaTrans.storage

cd $WICRI_ROOT/Bois/explor/PlantGlutaTrans.storage

NlmPubMedExplorCorpus  -d PlantGlutaTransV1   \
          -q "plant glutathione transferases" -s 250    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration Glutathion S-transférase végétale"

cas complexe: réécriture de la requête

NlmPubMedGetCorpusSize -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("effector"[All Fields] OR "effectors"[All Fields])'

1029

mkdir $WICRI_ROOT/Bois/explor/PlantPathoEff.storage

cd $WICRI_ROOT/Bois/explor/PlantPathoEff.storage

NlmPubMedExplorCorpus  -d PlantPathoEffV1  \
         -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("effector"[All Fields] OR "effectors"[All Fields])' -s 250    \
          -l  wicri-bois.fr -p Bois \
          -t "Serveur d'exploration sur les effecteurs de phytopathogènes"

@@ Ligne 80 : / Ligne 80 : @@
 ===Retour machine locale===
 <source>
-NlmPubMedGetCorpusSize -q "biopesticide peptide"
+NlmPubMedGetCorpusSize -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'
-mkdir $WICRI_ROOT/Bois/explor/TreeMicInter.storage
+mkdir $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage
-cd $WICRI_ROOT/Bois/explor/TreeMicInter.storage
+cd $WICRI_ROOT/Bois/explor/RustFungiGenomicsV1.storage
-NlmPubMedExplorCorpus  -d TreeMicInterV1  \
+NlmPubMedExplorCorpus  -d RustFungiGenomicsV1   \
-           -q "(tree OR trees) AND (microbe OR microbic OR microbes) AND (interaction OR interactions OR interactivity OR interacts OR interactive)"   -s 8000    \
+           -q '"rust"[All Fields] AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields]) AND ("genome"[MeSH Terms] OR "genome"[All Fields] OR "genomes"[All Fields] OR "genome s"[All Fields] OR "genomically"[All Fields] OR "genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields])'   -s 8000    \
            -l  wicri-bois.fr -p Bois \
-           -t "Serveur d'exploration sur les interactions arbre microorganisme"
+           -t "Serveur d'exploration sur la génomique des pucciniales"
 </source>
 <source>
-NlmPubMedGetCorpusSize -q  NlmPubMedGetCorpusSize -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])'
+NlmPubMedGetCorpusSize -d -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])'
@@ Ligne 104 : / Ligne 104 : @@
 cd $WICRI_ROOT/Bois/explor//BiopestPeptid.storage
-NlmPubMedExplorCorpus  -d /BiopestPeptidV1  \
+NlmPubMedExplorCorpus  -d BiopestPeptidV1  \
-           -q  NlmPubMedGetCorpusSize -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])' -s 7000    \
+           -q '("biological control agents"[MeSH Terms] OR ("biological"[All Fields] AND "control"[All Fields] AND "agents"[All Fields]) OR "biological control agents"[All Fields] OR "biopesticides"[All Fields] OR "biopesticidal"[All Fields] OR "biopesticide"[All Fields]) AND ("peptid"[All Fields] OR "peptidal"[All Fields] OR "peptide s"[All Fields] OR "peptides"[MeSH Terms] OR "peptides"[All Fields] OR "peptide"[All Fields] OR "peptidic"[All Fields])' -s 7000    \
            -l  wicri-bois.fr -p Bois \
            -t "Serveur d'exploration sur les peptides biopesticides"
@@ Ligne 112 : / Ligne 112 : @@
 <source>
-NlmPubMedGetCorpusSize -q mycorrhizae
+NlmPubMedGetCorpusSize -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])'
-mkdir $WICRI_ROOT/Bois/explor/Mycorrhizae.storage
+mkdir $WICRI_ROOT/Bois/explor/RapamycinFungus.storage
-cd $WICRI_ROOT/Bois/explor/Mycorrhizae.storage
+cd $WICRI_ROOT/Bois/explor/RapamycinFungus.storage
-NlmPubMedExplorCorpus  -d MycorrhizaeV1  \
+NlmPubMedExplorCorpus  -d RapamycinFungusV1  \
-           -q mycorrhizae -s 6500    \
+           -q '("rapamycin s"[All Fields] OR "rapamycine"[All Fields] OR "rapamycins"[All Fields] OR "sirolimus"[MeSH Terms] OR "sirolimus"[All Fields] OR "rapamycin"[All Fields]) AND ("fungi"[MeSH Terms] OR "fungi"[All Fields] OR "fungus"[All Fields] OR "fungis"[All Fields] OR "microbiology"[MeSH Subheading] OR "microbiology"[All Fields])' -s 3500    \
            -l  wicri-bois.fr -p Bois \
-           -t "Serveur d'exploration sur la mycorhize"
+           -t "Serveur d'exploration sur la rapamycine et les champignons"
+</source>
+===Volumétrie croissante===
+;cas simple:
+<source>
+NlmPubMedGetCorpusSize -q "wood degradation fungi"
+mkdir $WICRI_ROOT/Bois/explor/WoodDegFungi.storage
+cd $WICRI_ROOT/Bois/explor/WoodDegFungi.storage
+NlmPubMedExplorCorpus  -d WoodDegFungiV1   \
+          -q "wood degradation fungi" -s 250    \
+          -l  wicri-bois.fr -p Bois \
+          -t "Serveur d'exploration sur les champignons de dégradation du bois"
+</source>
+<source>
+NlmPubMedGetCorpusSize -q "plant glutathione transferases "
+mkdir $WICRI_ROOT/Bois/explor/PlantGlutaTrans.storage
+cd $WICRI_ROOT/Bois/explor/PlantGlutaTrans.storage
+NlmPubMedExplorCorpus  -d PlantGlutaTransV1   \
+          -q "plant glutathione transferases" -s 250    \
+          -l  wicri-bois.fr -p Bois \
+          -t "Serveur d'exploration Glutathion S-transférase végétale"
 </source>
+;cas complexe:réécriture de la requête
 <source>
-NlmPubMedGetCorpusSize -q "grapevine disease"
+NlmPubMedGetCorpusSize -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("effector"[All Fields] OR "effectors"[All Fields])'
-mkdir $WICRI_ROOT/Bois/explor/GrapevineDisease.storage
+mkdir $WICRI_ROOT/Bois/explor/PlantPathoEff.storage
-cd $WICRI_ROOT/Bois/explor/GrapevineDisease.storage
+cd $WICRI_ROOT/Bois/explor/PlantPathoEff.storage
-NlmPubMedExplorCorpus  -d GrapevineDiseaseV1  \
+NlmPubMedExplorCorpus  -d PlantPathoEffV1  \
-          -q "grapevine disease" -s 2000    \
+         -q '("plant s"[All Fields] OR "planted"[All Fields] OR "planting"[All Fields] OR "plantings"[All Fields] OR "plants"[MeSH Terms] OR "plants"[All Fields] OR "plant"[All Fields]) AND ("pathogen"[All Fields] OR "pathogen s"[All Fields] OR "pathogene"[All Fields] OR "pathogenes"[All Fields] OR "pathogenic"[All Fields] OR "pathogenically"[All Fields] OR "pathogenicities"[All Fields] OR "pathogenicity"[MeSH Subheading] OR "pathogenicity"[All Fields] OR "virulence"[MeSH Terms] OR "virulence"[All Fields] OR "pathogenity"[All Fields] OR "pathogenous"[All Fields] OR "pathogens"[All Fields]) AND ("effector"[All Fields] OR "effectors"[All Fields])' -s 250    \
            -l  wicri-bois.fr -p Bois \
-           -t "Serveur d'exploration sur les maladies des plantes grimpantes"
+           -t "Serveur d'exploration sur les effecteurs de phytopathogènes"
 </source>

Discussion:Espace Interactions Arbres Microorganismes/Serveurs : Différence entre versions

Version actuelle datée du 21 novembre 2020 à 16:38

Sommaire

Protocole

Modèle de paramétrage

Sur machine locale (mac)

Sur VM LorExplor

Retour machine locale

Volumétrie croissante

Menu de navigation

Affichages

Outils personnels

Navigation

Rechercher

Outils