FoodMicrobionet2:Structureofedgesandnodestables1.
EugenioParente.DipartimentodiScienze,UniversitàdeglistudidellaBasilicata.
This document describes the structure of the edge and node tables for FoodMicrobionet.
Severalnewfieldshavebeenintroduced(andafewhavebeenremoved)comparedtoversion
1(Parenteetal.,2016).Mostofthenewfieldsaresomewhatredundantforuseinnetwork
visualisationsoftware(Gephi,Cytoscape)buttheydomaketheselectionofspecificsubsetsof
sampleorenvironmentalnodeseasier.Inaddition,mostofthenewfeaturesweredesignedto
facilitate processing of the tables with other software packages (Microsoft Excel, the CoNet
App of Cytoscape, the Bipartite package of R). To learn more on FoodMicrobionet visit our
websiteat:http://www.foodmicrobionet.org
TheedgestableincludesalistofallrelationshipsbetweenOperationalTaxonomicUnitsand
samples (food or food environment). The fields included in the current version of
FoodMicrobionetare:
1) Source(Food/foodenvironmentsample):thelabelofthefoodsample
2) Target (OTU): the taxonomic assignment including all the lineage in the format
Root:k__Bacteria__Firmicutes:c__Bacilli:f__Lactobacillaceae:g__Lactobacillus:s__Lactobacillu
sdelbrueckii.Currentversiondoesnotincludeorderasataxonomicrank
3) Type:thetypeoftherelationship;inFoodMicrobionetalledgesaresettoUndirected
4) id:anumericalidfortheedge,automaticallycreatedimportinginGephi
5) Gtarget1:thetargetusedforsequencing,either16S_DNAor16S_RNA2
6) Gtarget2:thevariableregionsof16SrRNAgenetargetedbyPCRamplification
7) Study:thenumberofthestudy,seeFMBNProjectTable3
8) OTULabel:alabelforthetargetnode(speciesifavailable,otherwisethefirstvalidtaxon;
Otherifunidentified).ThisfieldisnotneededforGephibutcanfacilitatetheuseoftables
withthelibrarybipartite
9) Weight:theOTUabundanceinthesamples(as%)
The nodes table includes metadata for nodes. The current version of FoodMicrobionet
includesthefollowingfields:
1) Id:auniquevaluematchingeitherasourceortargetnode.
2) Label: this column contains the node display label; same as Target for the OTUs;
constructedbycombiningSourceandfurtherinformationforfood/environmentsamples
3) Type:setto"OTU"fornodescorrespondingtoOTUs,"Sample"fornodescorrespondingto
foodsamples,and"Environment"forsamplesfromfoodenvironments.
4) Llabel: a "long" label. For Sample and Environment nodes incorporates information on
FoodIDandFoodstatus(seebelow)ina8characterformat(5charactersfortheFoodID
1changesfromversion1.0areinred
2technically,boththesefieldscouldbemovedtothenodetable;thissetupisequivalentinGephi(thesame
samplecanhaveresultsonbothDNAandRNAextraction)butmaybesomewhatawkwardwithothersoftware
packages
3thenumberofthestudyisassignedasstudiesareintroducedinFoodMicrobionet.Itcanbeusedforrapid
selectoinofedges.Althoughitisredundantinthistable(nodescanbeselectedmoreeasilybyusingthesame
fieldinthenodepage)itisusefultoextractabundancetablesfromtheedgetablefile.
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and 3 for food status, see below for abbreviations). Useful for labelling nodes in some
instancesandtopassinformationtofilestobeusedforthebipartitepackage.
5) Study:thenumberofthestudy(seeabove)(forSampleandEnvironmentnodes,settoNA
forOTUnodes):thiscanbeusedforrapidselection.
6) Nreads:numberofreadsafterclean-up,settoNAforOTUs,#N/Difnotavailable
7) Shannon:Shannondiversityindex,settoNAforOTUs,#N/Difnotavailable
8) Chao1:Chao1diversityindex,settoNAforOTUs,#N/Difnotavailable
9) Nreads2:adummyvalue(2999)tobeusedforsamples(foodorenvironment)ifNreads
isnotavailable,otherwiseNreads;thisvalueisusedtorebuildOTUtableswithabsolute
frequenciesstartingfromtheedgeandnodetables
10)Bioproject: the accession number of the sequences if available, set to NA for OTU and
NONEwhennotavailable
11)Study:seeedgetable,settoNAforsamplenodes
12)Ontologycolumns,OTUs:thesefieldsaresettoNAforsamplenodes.
a) Domain: only needed in studies in which more than one domain is retrieved, Set to
Bacteria
b) Phylum:ifavailable,otherwisesettothevalueforDomain;
c) Class:ifavailable,otherwisesetto"Other";
d) Family:ifavailable,otherwisesetto"Other";
e) Genus:ifavailable,otherwisesetto"Other";
f) Species:Species,ifavailable,otherwisesettothefirstvalidtaxon
g) Taxlevel: a string field representing the identification level achieved (species, genus,
family,class,phylum)forfilteringpurposes
13)DOI:theDOIofthearticlewherethestudyincludingthedatawasoriginallypublished;set
toNONEiftheworkisunpublishedandNAforOTUs
14)Outlink1:thisfieldcontainsalinktoexternalresources.Itiscurrentlysettoapointerto
the DOI for the paper where the data were originally published (NA for unpublished
papers)forsamplenodesoralinktoNCBItaxonomyforOTUnodes.
15)Outlink2:thisfieldcontainsalinktoexternalresources.Itiscurrentlysettoapointerto
the study (NA when not available) in SRA for sample/environment nodes or a link to
bacterio.netforOTUnodes.
16)Ontologycolumns,samples/environment:thesefieldsaresettoNAforOTUnodes;the
hierarchicaltermsandIDsarederivedfromthefoodclassificationanddescriptionsystem
FoodEx2(draft-revision1)adoptedbytheEuropeanFoodSafetyAuthority(EFSA,2011).
For food environments these are set to the same values of the food processed in that
environment.4
a) FoodCat:thefoodmacrocategory
b) FoodGroup:thefoodgroup
c) Foodsubgroup1: the food subgroup in FoodEx 2 if available, otherwise
Foodsubgroup1isused
d) Foodsubgroup2: the lowest classification level in FoodEx 2 if available, otherwise
Foodsubgroup1isused
e) FoodID:thealphanumericalFoodIDcodeinFoodEx2
4thereisanissuewithfoodsamplesobtainedduringprocessingof,forexample,ahard,ripenedcheese.A
cheesecurdisquiteobviouslyacompletelydifferentenvironmentcomparedtoamaturehardcheese.Thisissue
isdealtwithbythe"Nature"field;whenthecorrectclassificationisnotfoundinFoodExtheclostestrelativeis
used
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f) FoodType: a shorter list of food groups with items Bakery items, Beef, Beverages,
Dairy products, Eggs, Fishery products, Multi-ingredient foods, Other, Pork , Poultry,
Produce(includingfruits)
17)Foodstatuscolumns:thesecolumnsdescribethestatusofthefoodsample(NAforOTUs
andenvironmentalsamples,shorthandforLLlabel0)
a) Nature: Raw (raw material or ingredient), Intermediate, Finished (including the
productsduringstorage)(shorthandsr,i,f)
b) Process: None (raw materials and foods other than those covered by the other
options); Mild (foods with no physical lethal treatment; includes foods with added
preservatives, mild heat treatments and fermentation); Type2 (foods submitted at
leasttoalethaltreatmentresultingpotentiallyina6DdecreaseinL.monocytogenes,
but whose treatment is lower than that of type 1 foods; in these foods the heat
treatmentinbetween70°Cfor2minand90°Cfor10min);Type1(foodssubmittedat
leasttoalethaltreatmentresultingpotentiallyina6DdecreaseinC.botulinumtypeE
spores,approximately90°Cfor10minorequivalent)5.ShorthandsforLLabel:n,m,2,
1
c) Spoilage:6 NA (no information available), Unspoiled (all fresh or processed, non
spoiled foods); Fermented (all unspoiled fermented foods), Spoiled (all nonfermentedfoodswhicharespoiledorareattheendofshelf-life),Fermented+spoiled
(fermented foods which are also spoiled or at the end of shelf-life). Shorthands for
LLabel:0,u,f,s,b.
18)Selection fields: these fields are used for partitioning, searching and applying styles to
bothOTUandsamplenodes
a) Custom1: set to FoodCat and phylum for sample/environment and OTU nodes,
respectively
b) Custom2: set to FoodGroup and class for sample/environment and OTU nodes,
respectively
c) Custom3: set to family for OTU nodes; for sample/environment nodes a description
including Food subgroup terms or nature of the environmental samples with further
informationprovidedbytheauthorsofthestudy
References.
• EFSA(2011).ThefoodclassificationanddescriptionsystemFoodEx2(draft-revision
1).Supportingpublications2011:215.
http://www.efsa.europa.eu/en/supporting/pub/215e.htm
• Parente,E.,Cocolin,L.,DeFilippis,F.,Zotta,T.,Ferrocino,I.,O'Sullivan,O.,Neviani,E.,
DeAngelis,M.,Cotter,P.D.,ErcoliniD.(2016).FoodMicrobionet:Adatabaseforthe
visualisationandexplorationoffoodbacterialcommunitiesbasedonnetworkanalysis.
InternationalJournalofFoodMicrobiology,219,28–37.
http://doi.org/10.1016/j.ijfoodmicro.2015.12.001
5thisisapplicabletoreadytoeatfoods.Bothtype1andtype2mayincludefermentedfoodswhichhavebeen
submittedtoaheattreatmentACMSF,2007.Reportonsafecookingofburgers. Retrievedfrom
http://www.food.gov.uk/multimedia/pdfs/acmsfburgers0807.pdf.
6includesfoodsattheendofshelflife,eveniftheydonotshowclearspoilage.
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