Uploading Unit IDs in Batch on the EarthCape Cloud
Last updated: 16th March 2018
(NB These are instructions for uploading using the windows client. In future releases it will be possible to upload Unit IDs via the cloud and this website will be updated accordingly).
Before you start:
- Obtain UnitIDs (and unique) for your samples. These should have already have been given these, or else speak to someone running the database (currently Ian) to allocate you the appropriate IDs.
- Check your UnitIDs are not already being used. If you have been allocated unit IDs they should not be in the database, but it is worth checking. Use a filter list or a simple search of the database to check their presence.
- This is only possible by people with both a user ID.
Step 1: Create a spreadsheet
The template for the spreadsheet can be found at on the dropbox folder at:
Also see the attached sample file
There are many columns you can add data to, with some common column headers being shown in the table below.
|UnitID (Essential)||CAM009223||This is for the Unit ID|
|Sequence||9223||For the Cambridge Collection (any UnitID beginning with “CAM”) this is the Unit ID without the “CAM”. This makes searching the database a lot easier.|
|TaxonomicName||Heliconius timareta ssp. timareta||This is the species name. Please check your species name is already present on the database and spelled correctly. NB The dot after “ssp” is VERY important!|
|Locality||El Topo, Baños – Puyo road,||This is where the individual was collected. Please check the locality is present on the database and spelled correctly (also see warning below).|
|AccessionEna||ERS977721||If the individual has been used for sequencing add the ENA Sample accession number (NOT the run accession number). Sample accession numbers start in SRS, ERS, or SAMN.|
|Comment||Yellow/Rays||This is for additional comments. This is a very useful place to keep any additional information about an individual. Eg alternative IDs. This is a non-additive, so any existing comments will be replaced.|
[appears on database as:
|Information on where the individual is kept. In the Jiggins group the nomenclature is as follows: “DrawerXX/YYY”. Where XX = the drawer in the -80 freezer, and YYY is the number of the box. For the upload sheet only write the box number (“YYY”). Also check that box is present on the database.|
Step 2: CHECK THESE WARNINGS
- WARNING 1: Check spelling and check the presence of your input data for the following columns: TaxonomicName, Locality, Store, Dataset. If they are not present, then add them before uploading the units. See how to do this elsewhere.
- WARNING 2: Check for accents. If there are any accents in any of your fields, then note them down. Excel cannot code letters with accents very well. In order to correct this, open your csv file in a basic text editor (notepad, textwrangler etc) and adjust the accents there.
Step 3: Practice upload (Recommended)
To test that the upload spreadsheet is going to work, take two 2-3 units (and the column headers) from your upload file, and paste them into a new spreadsheet and save it with a different name.
Step 3.1 Log onto EarthCape Cloud
This is the link to the database https://heliconius.ecdb.io/
Move the cursor to hover over the word “Anonymous”, in the top right corner, and the “login” box will appear.
Step 3.2: Move to the Units part of the database
The link for Units can be on the left hand menu.
Step 3.3: Under more options (…) select “Import”
Step 3.4: Click on the white box to select a file to the file select prompt.
Step 3.5: Select Browse and find your file
Step 3.6: Press “OK” at both prompts
Step 3.7: A sign will come up to tell the import was successfull
If there is a problem, an error message will be produced.
Step 3.8: Check that the files have been uploaded correctly.
Step 4: Upload all of your data
If you are happy with your practice run, then upload all of your data, following the stages listed in Step 3 but using your main upload file instead.