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MAR-ECO data to OBIS

MAR-ECO data to OBIS

Here are some brief info about our data exchange with OBIS ( As known for most of you, MAR-ECO is trough the Census Of Marine Life, obligated to deliver data to the

OBIS system. The data OBIS require are at distribution level (taxa, number and position). The data are quite easy to extract and should not add so much extra workload to the people including the data into the database. However the data have to be in the official "MAR-ECO Biotic database".

We use the "Revision" field to determine witch data we want to transfer to OBIS. Codes used in the Revision field:

A = Cruise id accepted
R = Revised
C = Confirmed
pen = Pending
MSR = Main sample revised
MSC = Main sample confirmed
Blank is also used for unrevised, unconfirmed or working samples

Only records marked with C, R and A will be extracted to OBIS


We have now established the dataflow for transferring data to OBIS. After an extra effort from the fish group, the first "dataset" allmost all the fish observations are made available for OBIS.

Further work

It’s time to focus to start prepare new data for OBIS.

Sea mammal and bird data

These data are almost ready to transferee to OBIS. All the data are revised as A (Cruise id accepted). However some work has to be done with taxa names etc. Data should be available for OBIS within October this year.

Invertebrate data

There has been done a lot of work on the invertebrates. However there are a lot to do before all data can be available for OBIS. The plan will be to start with some animal groups. After the Cephalopod workshop i Bergen this autumn, we will start to update the database and make the data available for OBIS, hopefully at the end of 2006.


Work done on the plankton will this autumn and the beginning of next year be transferred to the database. These data will then be made available for OBIS

Technical info:

When data are ready to extract to OBIS (new or updated), we run an SQL query to extract the data going to OBIS. These data are then transferred to an simple database outside our DMZ network. A program called DiGIR communicated with the OBIS system and makes the data available for the OBIS community.

SQL query - Search i the database, to extract OBIS data

SELECT "MAR-ECO - Bergen Museum, Norway" AS [Institution Code], [TBL_plattform].[PL_purpose], First([TBL_sampling].[SMP_labelnumber]) AS FirstOfSMP_labelnumber, [TBL_sampling].[SMP_taxon] AS [Scientific Name], 'The Census of Marine Life field project MAR-ECO, 2003-2005.' AS Citation, ROUND(Int([LS_latitude]/100)+([LS_latitude]/100-Int([LS_latitude]/100))*10/6,3) AS Latitude, (-1)*ROUND(Int([LS_longitude]/100)+([LS_longitude]/100-Int([LS_longitude]/100))*10/6,3) AS Longitude, [TBL_sampling].[SMP_MUS_revision]

FROM TBL_plattform INNER JOIN ((TBL_superstation_in_plattform INNER JOIN TBL_localstation ON [TBL_superstation_in_plattform].[SS_superstation]=[TBL_localstation].[LS_superstation]) INNER JOIN TBL_sampling ON [TBL_localstation].[LS_ID]=[TBL_sampling].[SMP_LS_ID]) ON [TBL_plattform].[PL_ID]=[TBL_superstation_in_plattform].[SS_PL_ID]

GROUP BY [TBL_plattform].[PL_purpose], [TBL_sampling].[SMP_taxon], ROUND(Int([LS_latitude]/100)+([LS_latitude]/100-Int([LS_latitude]/100))*10/6,3), (-1)*ROUND(Int([LS_longitude]/100)+([LS_longitude]/100-Int([LS_longitude]/100))*10/6,3), [TBL_localstation].[LS_superstation], [TBL_localstation].[LS_localstation], [TBL_localstation].[LS_serialnumber], [TBL_sampling].[SMP_MUS_revision]

HAVING (((TBL_sampling.SMP_MUS_revision) In ('C','R','A')))

ORDER BY [TBL_sampling].[SMP_taxon];



OBIS Schema:

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