Look-up tables for Sample metadata.
GenBank-ready fields
Each field is named <source>_<name>, for
example gbif_lat_lon. A field is empty for a sample unless
its required parts exist. For GEOME, each value comes from the nearest
record that has it (tissue, then sample, then event). GBIF fields come
from the occurrence only.
| Name | GEOME (geome_) |
GBIF (gbif_) |
NCBI (ncbi_) |
|---|---|---|---|
lat_lon |
decimalLatitude, decimalLongitude
|
decimalLatitude, decimalLongitude
|
lat_lon (a decimal pair is converted) |
collection_date |
yearCollected, monthCollected,
dayCollected
|
year, month, day; else a
single-date eventDate
|
collection_date |
geo_loc_name |
country, then stateProvince and
locality
|
country, then stateProvince and
locality
|
geo_loc_name |
specimen_voucher |
genbankSpecimenVoucher; else
institutionCode and catalogNumber
|
institutionCode, collectionCode,
catalogNumber
|
specimen_voucher |
collected_by |
collectorList |
recordedBy |
collected_by |
identified_by |
identifiedBy |
identified_by |
|
tissue_type |
tissueType |
||
sex |
sex |
sex (lowercased) |
sex (lowercased) |
dev_stage |
lifeStage |
lifeStage (lowercased) |
dev_stage (lowercased) |
Example values: lat_lon
17.48260 S 149.89990 W; collection_date
2006-03-18, 2009-11, or 2009;
geo_loc_name French Polynesia: Moorea;
specimen_voucher USNM:FISH:407263.
-
Vouchers. A catalog number that is a web address or
an ARK gives an empty voucher. GBIF vouchers drop a leading repeat of
the institution code (
USNM 419933becomesUSNM:FISH:419933). -
NCBI placeholders such as
missing,not collected, ornot providedgive an empty value.
NCBI also offers fields that insert the [BioSample=] and
[BioProject=] header tags, which GenBank uses to link the
record to those projects:
| Name | Built from | Example |
|---|---|---|
ncbi_biosample |
BioSample accession | SAMN29555051 |
ncbi_bioproject |
first BioProject of the BioSample | PRJNA720393 |
ncbi_biosample_sra |
the SRA record’s biosample
|
SAMN29555051 |
ncbi_bioproject_sra |
the SRA record’s bioproject
|
PRJNA720393 |
A BioSample can belong to several BioProjects; check that
ncbi_bioproject is the one for your submission. The
_sra fields are filled only for samples linked through an
SRA accession.
Raw fields
Every other field in a fetched record is available as
<source>_<Level>_<field>, for example
geome_Tissue_tissueType,
gbif_Occurrence_occurrenceID, or
ncbi_BioSample_isolate.
GBIF notes
GBIF interprets the records it publishes, so check its values before submitting:
-
gbif_lat_lonis empty when GBIF flags the coordinatesZERO_COORDINATE,COORDINATE_INVALID, orCOORDINATE_OUT_OF_RANGE. - Other flags keep the value but are shown as badges in the viewer.
Check values flagged
PRESUMED_SWAPPED_COORDINATE,PRESUMED_NEGATED_LATITUDEor_LONGITUDE,COORDINATE_REPROJECTED,COORDINATE_ROUNDED, orCOUNTRY_COORDINATE_MISMATCH. - Coordinates of sensitive species may be deliberately generalized.
Check the
dataGeneralizationsandcoordinateUncertaintyInMetersraw fields. - GBIF’s
countryis its own English name (United States of America), not always the name GenBank expects (USA). Checkgeo_loc_nameagainst GenBank’s country list. -
identifiedByand the GBIF taxon describe the museum specimen, which may differ from your identification of the sequenced tissue.
Mapping-file columns used by Compare
The Compare tab finds your mapping-file columns by name, ignoring
case. The first match wins. Use set_metadata_columns() or
Mapfile columns… when yours differ.
| Item | Columns tried |
|---|---|
| coordinates |
lat_lon; or a latitude column (lat,
latitude, decimalLatitude) plus a longitude
column (lon, long, longitude,
decimalLongitude) |
| collection_date |
collection_date, date,
eventDate
|
| country |
country, geo_loc_name (the part before
:) |
| locality | locality |
| voucher |
specimen_voucher, voucher,
catalogNumber
|
| collector |
collected_by, collector,
recordedBy
|
| sex | sex |
| dev_stage |
dev_stage, life_stage,
lifeStage
|
| taxon |
Taxon (always) |
NCBI’s country and locality come from the two parts of
geo_loc_name, and its taxon from the BioSample
organism.
Voucher search fields
When linking searches GBIF for a voucher, it reads:
| Record | Fields |
|---|---|
| NCBI BioSample |
specimen_voucher, genbankSpecimenVoucher,
materialSampleID, voucherCatalogNumber,
bio_material
|
| GEOME |
genbankSpecimenVoucher, materialSampleID,
voucherCatalogNumber, otherCatalogNumbers,
catalogNumber, or a bare voucherCatalogNumber
with the institutionID
|
Fetch messages
Shown in the viewer, when hovering a faded logo, or in the warning after a fetch.
| Message | Meaning |
|---|---|
BCID not found in GEOME |
No GEOME record has that ID. A typo in a well-formed BCID shows up this way. |
record is private or needs a GEOME login |
The record belongs to a private GEOME project. |
BCID not recognized by GEOME |
GEOME rejected the ID as malformed. |
'x' is not a GEOME BCID (expected ark:/NNNNN/...) |
The value does not look like a BCID. |
GBIF occurrence not found (IDs can change when a dataset is republished) |
No GBIF occurrence has that gbifID. Look the specimen up again on gbif.org. |
'x' is not a GBIF occurrence ID (expected digits) |
The value is not a gbifID or gbif.org link. |
BioSample ... not found,
SRA accession ... not found
|
NCBI has no record with that accession. |
SRA accession ... has no linked BioSample |
Supply the BioSample accession instead. |
'x' is not a BioSample or SRA accession (...) |
The value is not a recognized NCBI accession. |
could not reach GEOME / GBIF / NCBI (...) |
No connection. Try again later with fetch_*() or
Refresh all. |
GEOME / GBIF / NCBI returned HTTP ... |
Any other server error, often a busy server. Try again later; for
NCBI, set an API key (ncbi_api_key at setup). |
N possible GBIF matches for ...; not linked |
Linking found several GBIF specimens for a voucher. Paste the right gbifID. |
... record links to ...; kept your ID ... |
A fetched record names a different ID than yours. Check which is right. |