Usage of BODC parameter vocabularies INSPIRE Marine Pilot Meeting, Delft 31.08.2015

Where to find the vocabularies Parameter lists Overview Introduction Where to find the vocabularies Parameter lists How to use the vocabularies Some comments 31.08.2015

Introduction BODC provides vocabulary web services for access to oceanographic standard terms Vocabularies have been used by the SeaDataNet (SDN) community – a network of 45 marine organisations/data centres from 35 countries – since more than 10 years Vocabularies are hosted by BODC, but governed by various organisations Much improvement and extensions in recent years New NERC Vocabulary Server version 2.0(NVS2.0) – using SKOS for encoding data dictionareis and taxonomies – has been in use by the SeaDataNet and EMODNet community since 2013 31.08.2015

Introduction The relevant BODC parameter vocabularies for MSFD data reporting are P02 - SeaDataNet Parameter Discovery Vocabulary P01 - BODC Parameter Usage Vocabulary P35 - EMODNET chemistry lot aggregated parameter names (governed by EMODNet Chemistry) The P01 parameter list is already in the INSPIRE code list registry (http://inspire.ec.europa.eu/codelist/BODC_P01ParameterUsageValue/) 31.08.2015

Where to find the vocabularies SeaDataNet created a vocabulary website to help project partners to understand and to find the required terms and codes Presently BODC is testing a new vocabulary search tool (available on beta release) to serve users from projects other than SDN and it is P01-friendly http://seadatanet.maris2.nl/v_bodc_vocab_v2/welcome.asp https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/ 31.08.2015

Parameter Lists P02 - SeaDataNet Parameter Discovery Vocabulary is a generic term for groups of parameters. quite coarse grained and is essentially used for “data discovery” Example ‘MTWD’ – ‘Dissolved metal concentrations in the water column’ does not differentiate between the various metal parameters Not suitable for describing the parameters involved in the data ‘MTWD’ has more than 200 narrower P01 terms 31.08.2015

Parameter Lists The SeaDataNet website for the BODC vocabularies (http://seadatanet.maris2.nl/v_bodc_vocab_v2/welcome.asp) helps the user to understand the relationship between P02 and P01. 31.08.2015

Parameter Lists View P02 ‚MTWD‘ using SeaDataNet vocabulary portal 31.08.2015

Parameter Lists P01 - BODC Parameter Usage Vocabulary is finer grained (narrower) and gives a detailed description on the parameter together with methodologies, matrix and species etc. Example 1 ‚CBIOM004‘ – ‘Concentration of lead {Pb CAS 7439-92-1} per unit wet weight of biota {Limanda limanda (ITIS: 172881: WoRMS 127139) [Sex: female Size: length 200-249mm Subcomponent: liver]}‘ Example 2 ‚CHACHPXT‘ – ‘Concentration of chlorophyll-a {chl-a} per unit dry weight of sediment by acetone extraction and high performance liquid chromatography (HPLC)’ 31.08.2015

Parameter Lists P35 - EMODNET chemistry lot aggregated parameter names SeaDataNet and EMODNet Chemistry community realised that the P01 list would one day become unmanageable due to inclusion of the associated methods. The idea to exclude the method from the parameter description evolved gradually. Together with the new BODC vocabulary version NVS2.0 the aggregated list P35 came into existence. Example ‘EPC00105’ – ‘The amount of the pigment chlorophyll-a contained in the particulate material of a specified volume of any body of salt or fresh water’ has 46 narrower P01 terms. 31.08.2015

Parameter Lists View P35 ‚EPC00105 ‘ using SeaDataNet vocabulary portal 31.08.2015

How to use the vocabularies The SeaDataNet vocabulary website is more friendly for the eyes to read. The new BODC vocabulary search tool includes more useful technical details. http://seadatanet.maris2.nl/v_bodc_vocab_v2/welcome.asp https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/ 31.08.2015

How to use the vocabularies The description (preferred label) of P01 is set together by text modules in the following order: Measurement: e.g. ‘Concentration’ Substance: e.g. ‘lead’ Measurement Matrix Relationship: e.g. ‘per unit wet weight’ Matrix: e.g. ‘biota’ Matrix Subcomponent: e.g. ‘liver’ Taxon: e.g. ‘Limanda limanda (ITIS: 172881: WoRMS 127139)’ Organism Name: e.g. “Limanda limanda” Organism Specifics: e.g. ‘Sex: female Size: length 200-249mm’ Technique: e.g. ‘inductively-coupled plasma mass spectrometry’ 31.08.2015

How to use the vocabularies Free Search using SeaDataNet vocabulary portal It is quite simple to find the required parameter concept by entering into the ‘Free search’ field specific keywords separated by ‘%’ in the given order of the text modules. For example entering chlorophyll-a%water%filtration%hplc into the free search field returns only 41 instead of 291 entries for the keyword “chlorophyll”. ’HPLC’ is the methodology ‘High Performance Liquid Chromatography’. e.g. http://seadatanet.maris2.nl/v_bodc_vocab_v2/search.asp?lib=P01 31.08.2015

How to use the vocabularies The BODC URLs are structured as follows: To fetch the whole controlled vocabulary http://vocab.nerc.ac.uk/collection/LIST/VERSION/ URLs for the current contents of the 3 parameter vocabularies: To fetch a single concept http://vocab.nerc.ac.uk/collection/LIST/VERSION/CONCEPT/ Example for chlorophyll concentration from P02 list: http://vocab.nerc.ac.uk/collection/P02/current/ http://vocab.nerc.ac.uk/collection/P02/current/CPWC/ http://vocab.nerc.ac.uk/collection/P01/current/ http://vocab.nerc.ac.uk/collection/P35/current/ 31.08.2015

How to use the vocabularies Example to demonstrate the various degrees of complexity for the parameter “chlorophyll” in the 3 parameter lists. 1) P02 List: The URL for the current version of the P02 term for ”Chlorophyll pigment concentrations in the water column” is: This URL resolves to an XML document with SKOS elements where all narrower (P01 parameters with full description, P07 Climate and Forecast standard names) and broader (P03 SeaDataNet parameter groups) resources are specified. http://vocab.nerc.ac.uk/collection/P02/current/CPWC/ 31.08.2015

How to use the vocabularies 2) P01 List: The URL for the current version of the P01 term for “Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and manufacturer's calibration applied” is: This URL provides a full description of the parameter including unit, methodology and relationship to other controlled vocabularies like P35. http://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/ 31.08.2015

How to use the vocabularies http://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/ <rdf:RDF> <skos:Concept rdf:about="http://vocab.nerc.ac.uk/collection/P01/current/CPHLPM01/"> <skos:prefLabel xml:lang="en">Concentration of chlorophyll-a {chl-a} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and manufacturer's calibration applied</skos:prefLabel> <skos:altLabel xml:lang="en">chl-a_water_ISfluor_manufctrcal_sensor1</skos:altLabel> <skos:definition xml:lang="en">In-situ fluorometer with manufacturer calibration applied. </skos:definition> <dc:identifier>SDN:P01::CPHLPM01</dc:identifier> <dce:identifier>SDN:P01::CPHLPM01</dce:identifier> <skos:notation>SDN:P01::CPHLPM01</skos:notation> <owl:versionInfo>3</owl:versionInfo> <dc:date>2014-06-30 08:56:54.0</dc:date> <skos:note xml:lang="en">accepted</skos:note> <owl:deprecated>false</owl:deprecated> 31.08.2015

How to use the vocabularies <owl:sameAs rdf:resource="http://vocab.nerc.ac.uk/collection/P09/current/FLU2/"/> <skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/P02/current/CPWC/"/> <skos:related rdf:resource="http://vocab.nerc.ac.uk/collection/P06/current/UMMC/"/> <skos:broader rdf:resource="http://vocab.nerc.ac.uk/collection/P35/current/EPC00105/"/> <void:inDataset rdf:resource="http://vocab.nerc.ac.uk/.well-known/void"/> </skos:Concept> </rdf:RDF> P02: CPWC = Chlorophyll pigment concentrations in the water column P06: UMMC = Milligrams per cubic metre P35: EPC00105 = Water body chlorophyll-a 31.08.2015

Parameter Lists 3) P35 List: The URL for the current version of the P35 term for “The amount of the pigment chlorophyll-a contained in the particlate material of a specified volume of any body of salt or fresh water” is: Similar to P02 this P35 URL resolves to an XML document with SKOS elements where all related (P06 unit), narrower (P01 parameters with full description) and broader (P36 chemical group) resources are specified. http://vocab.nerc.ac.uk/collection/P35/current/EPC00105/ 31.08.2015

Some comments Advantage of ICES parameter list: Separation of methodology (analysis, pre-treatment, chemical extraction etc. have extra code lists) from parameter More flexible Thank you! Any questions? Advantage of BODC vocabularies Support form BODC vocabulary team (expert for each discipline) Expansion of vocabulary any time P01 already in INSPIRE code list registry P35 could be used as compromise between P02 and P01 31.08.2015