Include newly found term URI's from #4, except biomass

logsheet_schema_extended.csv

@@ -30,13 +30,13 @@
 ,"magnesium_method","xsd:string","xsd:string",,,"NA","NA",,"soil","Measured","optional","Method for the measurement of the concentration of magnesium in the sample. Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","according to doi",,
 ,"methane","xsd:float","xsd:float",,,"http://vocab.nerc.ac.uk/collection/P01/current/CH4CGMMX/ for soil and http://vocab.nerc.ac.uk/collection/P01/current/CH4CGCXX/ for water","umol/l","http://vocab.nerc.ac.uk/collection/P06/current/UPOX/","soil","Measured","optional","Methane (gas) amount or concentration at the time of sampling",8,,"says concentration or amount, but allows only one unit - so this is concentration or amount, cannot be both. Need to chose one from https://vocab.seadatanet.org/bandit/browse_step.php?&step=001methane_006S0600045 ; ok yes, then concentration which is also correct with our units http://vocab.nerc.ac.uk/collection/P01/current/CH4CGCXX/ NOTE: it specifies it differently if it refers to sediment: http://vocab.nerc.ac.uk/collection/P01/current/CH4CGMMX/ but we have the same term for water and sediment. can we only have the triples different?"
 ,"methane_method","xsd:string","xsd:string",,,"NA","NA",,"soil","Measured","optional","Method for the measurement of methane (gas) amount or concentration at the time of sampling. Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","according to doi",,
-"This will have to be transposed from a list to a set of separate columns, but we need still to figure out how to do that","n_alkanes","xsd:list ","xsd:list ",,"string+"" ""+float+"";""","NA","umol/l","http://vocab.nerc.ac.uk/collection/P06/current/UPOX/","water;soil","Measured","optional","Concentration of n-alkanes; can include multiple n-alkanes","n-hexadecane 100; n-hexatriacontane 201",,"will be hard to manage! also, cannot find anything in BODC for n-alkanes, tho can find many alkanes..."
+"This will have to be transposed from a list to a set of separate columns, but we need still to figure out how to do that","n_alkanes","xsd:list ","xsd:list ",,"string+"" ""+float+"";""","http://vocab.nerc.ac.uk/collection/P02/current/DALK/","umol/l","http://vocab.nerc.ac.uk/collection/P06/current/UPOX/","water;soil","Measured","optional","Concentration of n-alkanes; can include multiple n-alkanes","n-hexadecane 100; n-hexatriacontane 201",,"will be hard to manage! also, cannot find anything in BODC for n-alkanes, tho can find many alkanes..."
 """""","n_alkanes_method","xsd:list ","xsd:list ",,"string+"";""","NA","NA",,"water;soil","Measured","optional","Method for the measurement of the concentration of n-alkanes; can include multiple n-alkanes. Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","according to doi",,
 ,"nitrate","xsd:float","xsd:float",,,"http://vocab.nerc.ac.uk/collection/P01/current/NTRAZZXX/","umol/l","http://vocab.nerc.ac.uk/collection/P06/current/UPOX/","water;soil","Measured","optional","Concentration of nitrate in the sample",10.3,," "
 ,"nitrate_method","xsd:string","xsd:string",,,"NA","NA",,"water;soil","Measured","optional","Method for the measurement of the concentration of nitrate in the sample. Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","pretreatment description. photometrically. photometer brand",,
 ,"nitrite","xsd:float","xsd:float",,,"http://vocab.nerc.ac.uk/collection/P01/current/NTRIZZXX/","umol/l","http://vocab.nerc.ac.uk/collection/P06/current/UPOX/","water;soil","Measured","optional","Concentration of nitrite in the sample",0.12,," "
 ,"nitrite_method","xsd:string","xsd:string",,,"NA","NA",,"water;soil","Measured","optional","Method for the measurement of the concentration of nitrite in the sample. Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","pretreatment description. photometrically. photometer brand",,
-"This will have to be transposed from a list to a set of separate columns, but we need still to figure out how to do that","organism_count","xsd:list","xsd:list",,"string+"" ""+float+"";""","NA","will_need_to_define_ourselves","will_need_to_define_ourselves","water;soil","Measured","optional","Total cell count of any organism (or group of organisms) per volume of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","bacteria 551E-9;Synechococcus 136E-12","yes - but the unit, not the measurement","will be hard to manage if allowing multiple entries - hard to standardise - and if allowing multiple units. cant find a term in BODC for general cell count, only counts of certain organisms. We may need to define this ourselves and the cells being counted will get an aphiaID. also, 2 possible units"
+"This will have to be transposed from a list to a set of separate columns, but we need still to figure out how to do that","organism_count","xsd:list","xsd:list",,"string+"" ""+float+"";""","https://genomicsstandardsconsortium.github.io/mixs/0000103/","will_need_to_define_ourselves","will_need_to_define_ourselves","water;soil","Measured","optional","Total cell count of any organism (or group of organisms) per volume of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)","bacteria 551E-9;Synechococcus 136E-12","yes - but the unit, not the measurement","will be hard to manage if allowing multiple entries - hard to standardise - and if allowing multiple units. cant find a term in BODC for general cell count, only counts of certain organisms. We may need to define this ourselves and the cells being counted will get an aphiaID. also, 2 possible units"
 """""","organism_count_method","xsd:list","xsd:list",,"string+"";""","NA","NA",,"water;soil","Measured","optional","Method for the enumeration of total cell count of any organism (or group of organisms) per volume of sample, should include name of organism followed by the method (e.g. qPCR, atp, flow cytometry, microscopy, etc.). Provide as much information as possible. If there is a relevant reference or SOP, provide doi or link","bacteria Flow cytometry FACSAria II flow cytometer (Becton-Dickinson) and convertion factor described in Lee Fuhrman. 1987 ;Synechococcus Flow cytometry EPICS ALTRA. Beckman Coulter and convertion factor described in Kana Gliber. 2000",,
 " ","oxy_stat_samp","xsd:string","xsd:string",," ","https://www.ebi.ac.uk/ols/ontologies/envo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FENVO_00002045","NA",,"soil","Measured","optional","Oxygenation status of sample. Indicate if the sample is anaerobic by adding ""Y"" if anaerobic and ""N"" if not","Y","yes","http://purl.obolibrary.org/obo/PATO_0001455 (aerobic) and PATO:0001456 anearobic "
 ,"part_org_carb","xd:float","xd:float",,,"http://vocab.nerc.ac.uk/collection/P35/current/EPC00157/","ug/l","http://vocab.nerc.ac.uk/collection/P06/current/UGPL/","water;soil","Measured","optional","Concentration of particulate organic carbon",0.85,,
@@ -109,7 +109,7 @@ http://vocab.nerc.ac.uk/collection/P01/current/SO4XCLP1/"
 ,"organization","xsd:list","xsd:list",,"string+"";""","NA","NA",,"water;soil","Observatory","mandatory","Organization the observatory station belongs to","Institute of Marine Biology of the Rim (IMaBRi)",,
 ,"organization_country","xsd:string","xsd:string",,,"NA","NA",,"water;soil","Observatory","mandatory","Country the operating organization belongs to. Country names should be chosen from the INSDC country list (http://insdc.org/country.html)","France",,
 ,"organization_edmoid","xsd:list","xsd:list",,"integer+"";""","NA","NA",,"water;soil","Observatory","mandatory","Id of the operating organization according to the European Directory of Marime Organizations (EDMO). The EMDO ids can be found by using the EDMO search: https://edmo.seadatanet.org/search",5401,,
-,"project_name","xsd:string","xsd:string",,,"NA","NA",,"water;soil","Observatory","mandatory","Name of the project within which the sequencing was organized","EMOBON",,
+,"project_name","xsd:string","xsd:string",,,"https://genomicsstandardsconsortium.github.io/mixs/0000092/","NA",,"water;soil","Observatory","mandatory","Name of the project within which the sequencing was organized","EMOBON",,
 ,"sediment_type","xsd:string","xsd:string",,,"NA","NA",,"soil","Observatory","optional","Information about the sediment type based on major constituents","lithogenous","yes","should move the accepted terms (required value and units) to an EMO BON vocabulary; found ENVO terms, pls look at the previous tab"
 ,"so_id","xsd:string","xsd:string",,,"NA","NA",,"soil","Observatory","mandatory","Soft substrate sampling site id. This will be the sampling site id complemented by ""So""","JiJ554 So",,
 ,"tot_depth_water_col","xsd:float","xsd:float",,,"https://vocab.nerc.ac.uk/collection/P07/current/CFV13N17/","metre","http://vocab.nerc.ac.uk/collection/P06/current/ULAA/","water;soil","Observatory","mandatory","Measurement of total depth of water column in meters",42,,"this is for depth also, so ideally we need a different term here: is this a max possible depth? can we throw this out?"
@@ -147,7 +147,7 @@ http://vocab.nerc.ac.uk/collection/P01/current/SO4XCLP1/"
 ,"store_person_orcid","xsd:anyURI","xsd:anyURI","https://orcid.org/",,"NA","NA",,"water;soil","Sampling","optional","orcid URL of the person who is responsible for storage and shipment (if sample shipped) or for biobanking (if sample biobanked) (https://orcid.org)","https://orcid.org/0000-0002-0202-8256",,
 ,"store_temp_hq","xsd:float","xsd:float",,,"https://vocab.lternet.edu/vocab/vocab/index.php?tema=579&/temperature","celsius","http://vocab.nerc.ac.uk/collection/P06/current/UPAA/	","water;soil","Sampling","mandatory","Temperature at which sample was stored at the hq, e.g. -80 degree Celsius",-80,"yes","which one?"
 ,"tax_id","xsd:integer","xsd:anyURI","https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=",,"https://genomicsstandardsconsortium.github.io/mixs/0001320/","NA",,"water;soil","Sampling","mandatory","Taxonomy ID of the organism as in the NCBI Taxonomy database. Entries in the NCBI Taxonomy database have integer taxon IDs. For EMO BON seawater samples the NCBI taxonomy ID is 1874687 coresponsing to marine plankton metagenome.",1874687,"yes",
-,"tidal_stage","xsd:string","xsd:string",,,"NA","NA",,"water;soil","Sampling","optional","Stage of tide (if relevant), expected values are: low_tide, ebb_tide, flood_tide, high_tide, no_tide.","high tide","yes",
+,"tidal_stage","xsd:string","xsd:string",,,"https://genomicsstandardsconsortium.github.io/mixs/0000750/","NA",,"water;soil","Sampling","optional","Stage of tide (if relevant), expected values are: low_tide, ebb_tide, flood_tide, high_tide, no_tide.","high tide","yes",
 ,"time_fi","xsd:string","xsd:string",,,"NA","hour","https://vocab.nerc.ac.uk/collection/P06/current/UHOR/","water","Sampling","mandatory","Indicate here how long from sampling until filtration starts. If filtration takes place in the field, use ""fi"". Otherwise, indicate the time it takes to transfer samples in the lab in hours (h)",3,"yes",
 ,"failure","xsd:string","xsd:boolean",,"Convert T/F to 1/0","NA","NA","NA","w;s","Sampling","mandatory","Indicates if the data generation failed. Takes True (T) or False (F) values. If data generation from a material sample failed, it needs to be indicated here. The failure may have happened at any stage of the workflow.",,"yes",
 ,"scientific_name","xsd:string","xsd:string",,,"NA","NA","NA","w;s","Sampling","mandatory","Scientific name for the taxonomy ID of the organism as in the NCBI Taxonomy database. Entries in the NCBI Taxonomy database have integer taxon IDs. Each taxon ID cooresponds to a scientific name. For EMO BON seawater samples the NCBI taxonomy ID is 1874687 coresponding to ""marine plankton metagenome"". For EMO BON sediment samples the NCBI taxonomy is 412755 corresponding to “marine sediment metagenome” ",,"yes",