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my test

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---------

Co-authored-by: Daniel Hayes <[email protected]>
Co-authored-by: Callum Rollo <[email protected]>

README.md

@@ -5,7 +5,7 @@
 Here we review issues related to OceanGliders (OG) format and vocabularies.
 A discussion section is also available for any question or comment related to OG format and vocabulary.
 
-You can find the most recent version of the [OG format](https://oceangliderscommunity.github.io/OG-format-user-manual/)
+[Here](https://oceangliderscommunity.github.io/OG-format-user-manual/) is the most recent version of the user manual. 
 
 ### Example files
 

vocabularyCollection/agencies_role.md

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+| agencies_role | definition | status |
+|:------ |:------ |:------ |
+| funding agency | agency funding entire or part of the operation at sea, including any relevant aspect of the operation | pending |
+| operating agency | agency responsible for the operations at sea | pending |
+| data assembly center | agency responsible for the processing of the raw data acquired, including conversion into the community format | pending |
+| global data assembly cente | agency responsible for the collection of all OceanGliders data sets under the common format | pending |

vocabularyCollection/battery_type.md

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+| battery_type | definition | status |
+|:------ |:------ |:------ |
+| lithium rechargeable | Rechargeable lithium battery pack | pending |
+| alkaline rechargeable | Rechargeable alkaline battery pack | pending |
+| alkaline | alkaline battery pack | pending |
+| lithium | lithium battery pack | pending |
+| alkaline + lithium | alkaline and lithium battery pack | pending |
+| lithium primary |  | pending |

vocabularyCollection/contributors_role.md

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+| contributors_role | definition | status |
+|:--------- |:-------- |:--------- |
+| glider pilot | person (or one of the persons) piloting the glider during the mission | pending |
+| principal operator | person responsible for the operations from deployment to recovery of the glider. Operations do not cover piloting, data management and science | pending |
+| operator | person involved in operations from pre-deployment to recovery of the glider. Operations do not cover piloting, data management and science | pending |
+| principal investigator | person leading the scientific aspects of the glider mission | pending |
+| scientist | person involved in the scientific aspects of the glider mission | pending |
+| data manager | person responsible of the collection, processing and archiving of the data and metadata acquired during the glider mission | pending |
+| data curator | person responsible for overseeing the organization, maintenance, and quality of the dataset | pending |
+

vocabularyCollection/data_mode.md

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+| data_mode | descritpion | status |
+|:------ |:------- |:-------|
+| R | Real-time data. Data coming from the glider through a communication channel without physical access to the instruments, disassembly or recovery of the platform | pending |
+| P | Provisional data. Data obtained after the glider has been recovered or serviced | pending |
+| A | Real-time adjusted data. Real-time or provisional data that have been adjusted by real-time automatic procedures | pending |
+| D | Delayed-mode data. Data published after all calibrations and quality control procedures have been applied on the internally recorded or best available original data. This is the best possible version of processed data | pending |
+| M | Mixed data. This value indicates that the file contains data in more than one of the above states | pending |

vocabularyCollection/phase.md

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+| phase | description | status |
+|:----- |:------ |:------ |
+| ascent | the platform is moving up toward surface with no internal command on the pitch angle | pending |
+| descent | the platform is moving down toward targeted depth of operation with no internal command on the pitch angle | pending |
+| surfacing | the platform is drifting at the surface for communication, recovery or safety purpose | pending |
+| parking | the platform is maintained at a parking depth | pending |
+| inflexion | the platform is changing pitch angle to move from a phase to another | pending |
+| propelled | the platform momentum is increased by the propeller | pending |
+| transition | These particular points could be part of the previous as well as the following phase | pending |

vocabularyCollection/platform_maker.md

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+| platform_maker | definition | status |
+|:----- |:----- |:----- |
+| Teledyne Webb Research | [uri](http://vocab.nerc.ac.uk/collection/B75/current/ORG01077/)| pending |
+| Kongsberg Maritime AS | [uri](http://vocab.nerc.ac.uk/collection/B75/current/ORG00360/)| pending |
+| Scripps Institution of Oceanography | [uri](https://edmo.seadatanet.org/report/1390) | pending |
+| Alseamar | [uri](https://edmo.seadatanet.org/report/5241) | pending |
+| University of Washington | [uri](https://edmo.seadatanet.org/report/3839) | pending |
+| IRobot | [uri](http://vocab.nerc.ac.uk/collection/B75/current/ORG01747/) | pending |
+| Hydroid Inc. | [uri](http://vocab.nerc.ac.uk/collection/B75/current/ORG01760/) | pending |
+| Huntington Ingalls Industries | [uri](https://edmo.seadatanet.org/report/5678) | pending |
+| Hefring Engineering | Manufacturer of the Oceanscout glider model. [url](https://www.hefring.com/) | pending |

vocabularyCollection/platform_model.md

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+| platform_model | definition | status |
+|:------ |:------- |:------- |
+| Seaglider | Generic name for Seaglider models | pending |
+| iRobot Seaglider M1 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600025/) | pending |
+| UoW Seaglider M1 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600024/) | pending |
+| KM Seaglider M1 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600002/) | pending |
+| HYD Seaglider M1 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600026/) | pending |
+| UoW Seaglider M6 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600030/) | pending |
+| Slocum | Generic name for Slocum glider models | pending |
+| Slocum G1 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600013/) | pending |
+| Slocum G2 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600001/) | pending |
+| Slocum G3 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600014/) | pending |
+| Seaexplorer | Glider manufactured by Alseamar. [url](https://www.alseamar-alcen.com/index.php/products/underwater-glider/seaexplorer) | pending |
+| SIO Spray | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600027/) | pending |
+| SIO Spray2 | [uri](http://vocab.nerc.ac.uk/collection/B76/current/B7600028/) | pending |
+| OceanScout | Glider model manufactured by Hefring Engineering [url](https://www.hefring.com/oceanscout) | pending |

vocabularyCollection/platform_serial_number_prefix.md

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+| platform_serial_number_prefix | definition | status |
+|:------ |:------ |:------ |
+| unit | serial number prefix for Slocum  | pending |
+| sg | serial number prefix for SeaGliders | pending |
+| sea | serial number prefix for SeaExplorer | pending |
+| sp | serial number prefix for Spray | pending |

vocabularyCollection/platform_type.md

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+| platform_type | definition | status |
+|:------- |:------- |:------- |
+| sub-surface gliders |  http://vocab.nerc.ac.uk/collection/L06/current/27/ | pending |
+

vocabularyCollection/rtqc_method.md

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+| rtqc_method | definition | status |
+|:---------|:-------|:--------|
+| QUARTOD | [url](https://ioos.noaa.gov/project/qartod/) | pending |
+| ego quality control manual | [DOI](http://doi.org/10.13155/51485) | pending |
+| SOCIB QC manual | [DOI](https://doi.org/10.25704/q4zs-tspv) | pending |
+| gliders tools – SOCCO | [DOI](https://doi.org/10.3389/fmars.2019.00738) | pending |
+| UEA Seaglider toolbox | [url](https://bitbucket.org/bastienqueste/uea-seaglider-toolbox/src/toolbox/) | pending |
+| CoTeDe | [DOI](https://doi:10.21105/joss.02063) | pending |
+| ANFOG data management user's manual | [url](https://imos.org.au/fileadmin/user_upload/shared/ANFOG/ANFOG_DataManagement_UsersManual_v5_Nov28.pdf) | pending |

vocabularyCollection/sensor_model.md

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+| sensor_model | definition | status |
+|:----------|:----------|:----------|

vocabularyCollection/tableOfControlledVocab.adoc

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+[cols=",",options="header",]
+|===========================================================================================
+|image:figures/image1.png[image,width=164,height=144] a|
+OceanGliders 1.0 format - Vocabulary Collections
+
+|===========================================================================================
+
+////
+* [[Vocabulary Collections]]
+////
+== Vocabulary Collections
+The series of concepts of the https://github.com/OceanGlidersCommunity/OG1.0-user-manual[OG1.0 format] are controlled by a set of vocabulary collections managed by the OceanGliders data management team and other governance bodies. +
+These concepts are listed in the table below. Each concept is linked to its collection of vocabularies. Each collection has a status attribute. +
+[square]
+* The *pending* entries are being discussed by the community and are not yet supported by the OG1.0 format. +
+* The *validated* entries have been validated by the vocabulary working group and can be used in the OG1.0 format. +
+* The *published* entries have been published by the host when it exists. +
+
+Vocabulary collections that are not governed by OceanGliders do not follow the *status* convention described above.
+
+=== "host" and "governance" of the vocabulary collection
+
+**host** : The host is the entity that is serving the *published* vocabulary collections and enable machine to machine communication. +
+**governance** :  Governance refers to the entity in charge of the maintenance, evolution and publication of the vocabulary collection.
+
+=== Request a new entry
+**TO BE UPDATED WITH EMMA and NVS TEAM**
+
+To request a new entry in the table below, one should submit an issue to this repository entitle `*_new entry for table <name of the vocabulary>_*` . 
+The issue must indicate the value of the new entry and all its relevant attributes described in the corresponding table.
+
+=== Validation process
+
+A working group on controlled vocabulary collections will review the requests regularly.
+While a continuous update of the controlled vocabularies is anticipated, the working group will update the vocabulary collection at least twice a year.
+
+=== Table of controlled vocabularies
+
+|===
+|OceanGliders reference name | Collection name | OceanGliders subset | Request new terms | Governance 
+
+  | platform | https://vocab.nerc.ac.uk/collection/L06/current/[L06 - SeaVoX Platform Categories] |  https://vocab.nerc.ac.uk/collection/L06/current/27/[OceanGliders vocabulary subset] | https://github.com/nvs-vocabs/L06/issues | OceanGliders 
+  | institution | https://edmo.seadatanet.org/[EDMO code] |  No subset available for this collection | *tbd* | SeaDataNet 
+  | platform_serial_number_prefix | *tbd* | https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/serial_number_prefix.md[pending list] | *tbd* | OceanGliders
+  | program | *tbd* |  *tbd* | *tbd* | OceanOPS 
+  | oceangliders_site | *tbd* |  *tbd* | *tbd* | OceanOPS 
+  | contributors_role | *tbd* |  *OceanGliders vocabulary subset tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/contributors_role.md[pending list] | *tbd* | OceanGliders 
+  | agencies_role | https://vocab.nerc.ac.uk/search_nvs/C86/[C86 - SeaDataNet contact and security access roles] | *OceanGliders vocabulary subset tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/agencies_role.md[pending list] | *tbd* | OceanGliders 
+  | agencies_id | https://edmo.seadatanet.org/[EDMO code] | No subset available for this collection | *tbd* | SeaDataNet 
+  | naming_authority | https://edmo.seadatanet.org/[EDMO code] | No subset available for this collection | *tbd* | SeaDataNet 
+  | institution | https://edmo.seadatanet.org/[EDMO code] | No subset available for this collection | *tbd* | SeaDataNet 
+  | rtqc_method | https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/rtqc_method.md[Real Time Quality Control methods] | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/rtqc_method.md[pending list] | *tbd* | OceanGliders 
+  | phase_calculation_methodology | Phase calculation methods | *tbd* | *tbd* |OceanGliders 
+  | platform_model | https://vocab.nerc.ac.uk/search_nvs/B76/[B76 - BODC Platform Models] | *OceanGliders vocabulary subset tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/platform_model.md[pending list] | *tbd* | OceanGliders 
+  | ICES_code | https://vocab.ices.dk/?codetypeguid=7f9a91e1-fb57-464a-8eb0-697e4b0235b5[ICES reference table] | No subset available for this collection  | *tbd* | ICES 
+  | platform_maker |  http://vocab.nerc.ac.uk/collection/L35/current/[L35 - SenseOcean device developers and manufacturers] | *OceanGliders vocabulary subset tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/platform_maker.md[pending list] |  *tbd* | OceanGliders 
+  | battery_type | *tbd* | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/battery_type.md[pending list] |  *tbd* | OceanGliders 
+  | telecom_type |  https://vocab.nerc.ac.uk/search_nvs/R10/[*_e.g. R10 - Argo transmission systems_*]  | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/telecom_type.md[pending list] |  *tbd* | OceanGliders 
+  | tracking_system | *tbd* | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/tracking_system.md[pending list] |  *tbd* | OceanGliders 
+  | sensor_model | https://vocab.nerc.ac.uk/search_nvs/L22/[L22 - Seavox Device Catalog] |  https://vocabdev.nerc.ac.uk/scheme/GLIDER_SENSORS/current/[OceanGliders vocabulary subset] | https://github.com/nvs-vocabs/L22/issues | OceanGliders 
+  | data_mode | *tbd* | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/data_mode.md[pending list] |  *tbd* | OceanGliders 
+  | phase | *tbd* | *tbd* https://github.com/OceanGlidersCommunity/OG-format-user-manual/blob/vturpin-patch-3-VocabularyCollectionSection/vocabularyCollection/phase.md[pending list] |  *tbd* | OceanGliders 
+  | variable names | https://vocab.nerc.ac.uk/search_nvs/OG1/[OG1 - OceanGliders Parameter Usage Vocabulary] | https://vocab.nerc.ac.uk/search_nvs/OG1/ | https://github.com/nvs-vocabs/OG1/issues | OceanGliders 
+  | sensor type |  	http://vocab.nerc.ac.uk/collection/R25/current/[*_e.g. R25 - Argo sensor types_*]  | http://vocab.nerc.ac.uk/collection/R25/current/ | *tbd* | OceanGliders 
+
+
+|===
+
+* sensor type will be added to the list of control vocab in the format following emma exemplar.
+
+# Exemplars
+
+## Global attributes
+
+
+|===
+| Global attribute | Exemples 
+
+| platform | :platform = "sub-surface gliders";
+| platform_vocabulary | :platform_vocabulary = https://vocab.nerc.ac.uk/collection/L06/current/27/;
+| institution | :institution = "OGS";
+| institution_vocabulary | :institution_vocabulary = "https://edmo.seadatanet.org/report/120";
+*_HERE WE NEED TO ADD institution_vocabulary  IN THE FORMAT_*
+| program | :program = "OGS glider program" ;
+| program_vocabulary | :program_vocabulary = ;
+*_HERE WE NEED TO ADD program_vocabulary IN THE FORMAT_*
+| oceangliders_site | :oceangliders_site = "CONVEX";
+| oceangliders_site_vocabulary | :oceangliders_site_vocabulary = ;
+*_HERE WE NEED TO ADD oceangliders_site_vocabulary IN THE FORMAT_*
+| contributor | :contributor = "Elena Mauri,Silvina Logarzo"
+| contributor_role | :contributor_role = "principal investigator,Data scientist";
+| contributor_role_vocabulary | :contributor_role_vocabulary = "http://vocab.nerc.ac.uk/collection/W08/current/CONT0004/,http://vocab.nerc.ac.uk/collection/W08/current/CONT0006/";
+| agency | :agency = "OGS,CNR,Coriolis";
+| agency_vocabulary | :agency_vocabulary = "https://edmo.seadatanet.org/report/120,https://edmo.seadatanet.org/report/227,https://edmo.seadatanet.org/report/227";
+*_HERE WE NEED TO ADD agency_vocabulary IN THE FORMAT_*
+| agency_role | :agency = "operating agency,funding agency,data assembly center";
+| agency_role_vocabulary | :agency_role_vocabulary = ",,";
+
+|===
+
+## Variable Attributes
+### Platform Information
+*_Which option do we follow here?_*
+|===
+| Variable | Variable attribute | exemplar
+
+| PLATFORM_MODEL  |  
+
+:long_name = "model of the glider";
+
+:platform_model_vocabulary = "https://vocab.nerc.ac.uk/collection/B76/current/B7600002"; 
+
+
+
+:long_name = "model of the glider";
+
+:platform_model_vocabulary = "https://vocab.nerc.ac.uk/collection/B76/current/B7600001/"; |
+Kongsberg Maritime Seaglider M1 glider
+
+Teledyne Webb Research Slocum G2 glider
+
+| *OR* | | 
+
+| ICES_CODE | 
+:long_name = "Trieste_1";
+
+:ices_code_vocabulary = "https://vocab.ices.dk/?CodeID=230740"; | 
+
+
+
+| PLATFORM_MAKER | 
+:long_name = "Kongsberg Maritime AS";
+
+:platform_maker_vocabulary = "https://vocab.nerc.ac.uk/collection/B75/current/ORG00360/";
+
+
+
+:long_name = "Teledyne Webb Research";
+
+:platform_maker_vocabulary = "https://vocab.nerc.ac.uk/collection/B75/current/ORG01077/"; |
+|===
+
+
+https://github.com/OceanGlidersCommunity/OG-format-user-manual/edit/emma/Vocabs/src/vocabularyCollection/vocabulary_guidance.md[Check Emma's branch here]
+
+
+

vocabularyCollection/telecom_type.md

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+| telecom_type | description | status |
+|:------ |:------- |:------ |
+| iridium| Communication system based on IRIDIUM satellite constellation use by the glider when surfacing to relay to landstation (auto attendant computer) navigational fix, data and receive further instruction for command and control | pending |
+| freewave | Communication system based on Free Wave RF Modem (line of sight) use to relay to landstation (auto attendant computer) navigational fix, data and receive further instructions for command and control | pending |
+| argos | | pending |
+| cellular mobile | | pending |

vocabularyCollection/tracking_system.md

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+| tracking_system | description | status |
+|:------ |:------ |:------ |
+| gps | Global Positioning System is a satellite based radionavigation system | pending |
+| argos doppler | ARGOS constellation satellite-based system used to distribute location data | pending |
+| Beidou |  | pending |
+| acoustic | underwater location tracking | pending |

vocabularyCollection/variable_names.md

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+| variable_names| description | status |
+|:------ |:------ |:------|