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Preface
In context of MareHUB and the Viewer on marine-data.org data from different sources gets processed and provided as OGC Web Services. Mapping incoming data to unified names (target vocabulary) is part of this process. This page offers technical file specifications used during this process. It is not about the process (however, if in special cases there is process information, it is marked as such). For general information on processes, see the page on Standard Operating Procedures.
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Tables are color-coded. Input for the Mapping Algorithm has a light yellow, output a light blue background.
Version 0.1
There are two "types" of files. Those adding mapping rules and those introducing target vocabulary data can be mapped to. Mapping rules do not work without the according target vocabulary. Both are tab-separated files, only differing in column names.
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- tab-separated text file
- UTF-8-encoding
- file extension: .sdi.mapping.tab
- order of columns matter
- columns without values (e.g.
sphere_name) can be dropped - custom columns can be appended but will get ignored (might be useful for future verification, for example)
Target Vocabulary Files
Units
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | unit_name | yes | name of unit | degree Celsius Kelvin meter per second |
| 2 | unit_symbol | yes | symbol of unit | °C K m/s |
| 3+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
unit_name unit_symbol meter m square meter m² degree ° degree Celsius °C meter per second m/s centimeter per second cm/s |
Parameters
Column header for parameter vocabulary is parameter_group because currently it is used as rough grouping instead of precise mapping. However, both would be possible.
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | parameter_group | yes | name of parameter or parameter group | Temperature Total Organic Carbon |
| 2 | parameter_sdn | no | SDN of parameter | |
| 3 | parameter_nerc_uri | no | NERC URI of parameter | |
| 2+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
parameter_group Chlorophyll Salinity Sample ID Temperature |
Methods
Column header for method vocabulary is method_group because currently it is used as rough grouping instead of precise mapping. However, both would be possible.
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | method_group | yes | name of method or method group | direct count electric |
| 2+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
method_group ungrouped unspecified direct indirect count electric |
Spheres
Process information: Status Quo is NERC spheres. Please consult AG Ocean Obs (Norbert Anselm) and AG Viewer (Peter Konopatzky) before introducing other sphere vocabulary.
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | sphere_name | yes | name of sphere | atmosphere water body |
| 2 | sphere_sdn | no | SDN of sphere | |
| 3 | sphere_nerc_uri | no | NERC URI of sphere | |
4+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Status Quo
sphere_name | sphere_sdn | sphere_nerc_uri |
|---|---|---|
atmosphere | SDN:S21::S21S001 | |
water body | SDN:S21::S21S027 | |
surface ice | SDN:S21::S21S009 | |
rock | SDN:S21::S21S038 | |
biota | SDN:S21::S21S037 | |
not applicable | SDN:S21::S21S017 | |
Earth | SDN:S21::S21S006 | |
bed | SDN:S21::S21S003 | |
cave atmosphere | SDN:S21::S21S033 | |
experiment water sample | SDN:S21::S21S011 | |
geological sample | SDN:S21::S21S039 | |
groundwater | SDN:S21::S21S005 | |
peat | SDN:S21::S21S019 | |
rainwater | SDN:S21::S21S020 | |
sediment | SDN:S21::S21S022 | |
sediment pore water | SDN:S21::S21S023 | |
snow | SDN:S21::S21S024 | |
stalactite | SDN:S21::S21S034 | |
stalagmite | SDN:S21::S21S025 | |
suspended particulate material | SDN:S21::S21S026 | |
water body plus atmosphere | SDN:S21::S21S028 | |
wet sediment | SDN:S21::S21S031 |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
sphere_name sphere_sdn sphere_nerc_uri atmosphere SDN:S21::S21S001 http://vocab.nerc.ac.uk/collection/S21/current/S21S001/1/ water body SDN:S21::S21S027 http://vocab.nerc.ac.uk/collection/S21/current/S21S027/1/ surface ice SDN:S21::S21S009 http://vocab.nerc.ac.uk/collection/S21/current/S21S009/1/ rock SDN:S21::S21S038 http://vocab.nerc.ac.uk/collection/S21/current/S21S038/1/ biota SDN:S21::S21S037 http://vocab.nerc.ac.uk/collection/S21/current/S21S037/2/ not applicable SDN:S21::S21S017 http://vocab.nerc.ac.uk/collection/S21/current/S21S017/1/ Earth SDN:S21::S21S006 http://vocab.nerc.ac.uk/collection/S21/current/S21S006/1/ bed SDN:S21::S21S003 http://vocab.nerc.ac.uk/collection/S21/current/S21S003/1/ cave atmosphere SDN:S21::S21S033 http://vocab.nerc.ac.uk/collection/S21/current/S21S033/1/ experiment water sample SDN:S21::S21S011 http://vocab.nerc.ac.uk/collection/S21/current/S21S011/2/ geological sample SDN:S21::S21S039 http://vocab.nerc.ac.uk/collection/S21/current/S21S039/1/ groundwater SDN:S21::S21S005 http://vocab.nerc.ac.uk/collection/S21/current/S21S005/1/ peat SDN:S21::S21S019 http://vocab.nerc.ac.uk/collection/S21/current/S21S019/1/ rainwater SDN:S21::S21S020 http://vocab.nerc.ac.uk/collection/S21/current/S21S020/1/ sediment SDN:S21::S21S022 http://vocab.nerc.ac.uk/collection/S21/current/S21S022/2/ sediment pore water SDN:S21::S21S023 http://vocab.nerc.ac.uk/collection/S21/current/S21S023/1/ snow SDN:S21::S21S024 http://vocab.nerc.ac.uk/collection/S21/current/S21S024/1/ stalactite SDN:S21::S21S034 http://vocab.nerc.ac.uk/collection/S21/current/S21S034/2/ stalagmite SDN:S21::S21S025 http://vocab.nerc.ac.uk/collection/S21/current/S21S025/1/ suspended particulate material SDN:S21::S21S026 http://vocab.nerc.ac.uk/collection/S21/current/S21S026/1/ water body plus atmosphere SDN:S21::S21S028 http://vocab.nerc.ac.uk/collection/S21/current/S21S028/1/ wet sediment SDN:S21::S21S031 http://vocab.nerc.ac.uk/collection/S21/current/S21S031/1/ |
Mapping Rules Files
Output columns (light blue) need to hold target vocabulary established via target vocabulary files.
Unit Mapping
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | unit_string | yes | mapping input, any string that should get mapped | °C ◦C degC |
| 2 | unit_name | yes | mapping output: unit name (see Unit Vocabulary) | degree Celsius |
| 3+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
unit_string unit_name comment °C degree Celsius ◦C degree Celsius weird alternative degree character, found in GLODAP ?C degree Celsius broken encoding, found in COSYNA SOS degC degree Celsius cm/s centimeter per second |
Parameter Mapping
column | column header | value is mandatory | description | example values (all valid) |
|---|---|---|---|---|
| 1 | parameter_string | yes | mapping input, any string that should get mapped | Temperature Temperature, air WaterTemp_FSI |
| 2 | parameter_group | yes | mapping output: any known method name/group (see Parameter Vocabulary) | Temperature |
| 3 | sphere_name | no | mapping output: any known sphere name (see Sphere Vocabulary) | atmosphere |
| 4+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
parameter_string parameter_group sphere_name AirTemperature Temperature atmosphere SeaSurfaceTemperature Temperature TEMP_13.0 Temperature Temperature Temperature |
Method Mapping
column | column header | value is mandatory | description | example values |
|---|---|---|---|---|
| 1 | parameter_group | yes | mapping input: any known parameter name (see Mapping Names) | valid: Temperature invalid: WaterTemp_FSI |
| 2 | method_string | yes | mapping input: any string that should get mapped | valid: Mercury thermometer |
| 3 | method_group | yes | mapping output: any known method name/group (see Method Vocabulary) | valid: direct valid: unspecified valid: electrical |
| 4 | sphere_name | no | mapping output: any known sphere name (see Sphere Vocabulary) | valid: atmosphere valid: water body valid: sediment |
| 5+ | <whatever_you_like> | no | can be used for comments or notes/reminders – will get ignored technically |
Examples
| Code Block | ||||||
|---|---|---|---|---|---|---|
| ||||||
parameter_group method_string method_group sphere_name Chlorophyll High Performance Liquid Chromatography direct Chlorophyll Fluorometry indirect Chlorophyll Acetone extraction (Turner Designs) indirect |
Combined Example
Imagine you have the following data you want to have integrated into our SDI. It already comes in handy O2A GeoCSV format, including metadata files. Two data files (and two metadata files) with comparable datausing different vocabulary, and almost none of them using the vocabulary you want.
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