# List of known issues ### MARBEN - Missing `species` and `genus` columns ### General - References need manual review especially bibtex. Character encoding is still a recurring problem. Some references entities represent multiple references. * * * # Change log ## BioDeepTime v1.0 [2023-07-12] ### Added - new field `samples.totalCount` that represents the sample size in the case of count data, rather than the target sampling effort - Three new `abundanceUnit` categories: `"biomass cover"`, `"biomass weight"`, `"biomass volume"` - bibtex handles to the `bibtex` column of the `refs` table. The candidate bibtex entries are in the refs.bib file. ### Changed - The word occurrence was systmatically replaced with `record`. The `occurrences` table was renamed to `records`, its primary key from `occID` to `recordID`. - The `timeUnits` table was renamed to `timeOriginalUnits` for better consistency. Consequently, the the fields `timeUnitID` and `timeUnit` were rename to `timeOriginalUnitID` and `timeOriginalUnit`, respectively. - The `ranks` table was renamed to `analyzedRanks` for better consistency. - Reference entries are forced into UTF-8 encoding ##### BioTime - Omitted studies 39 and 217 due to potentially erroneous entries - Added biomass data to where there were no `abundanceUnit`s earlier - Time series taxonomic/environment groups are added - biomass values replaced abundance values in cases when count data was given as 0, but biomass was valid ##### Neotoma - sample sum count is moved to `samples.totalCount` from `samples.samplingEffort`. Accordingly `samplingEfforType` is consistently set to `NA`. - Neotoma references were split, multiple refs per samples are now properly indicated - Changed the taxon group to `Plants` ##### Triton - New version is used now - indicated to be released soon as Triton 2 - Fixed issues where all abundance values were relative abundances, even when count was indicated. - The sample sum is now recorded in `samples.totalCount` and not in `samplingEffort`. In case where samples reflect normalization for 1 gramm, the value 1 is now recorded in `samplingEffort` with a `samplingEffortType` of "g". ##### SedTraps - added missing `samplingEffortType` (all are m^2) ##### MARBEN - added `samplingEffort` and `samplingEffortType` values from `processing` - total count of count-type data - added missing reason: `"Community analysis"` - added reference to MARBEN ###### PBDB - added total count of count-type data ###### Direct uploads - coccolithophore data: moved total count from `samplingEffort` to `totalCount` ## Removed ###### BioTime - Studies 39 and 217 were removed due to quality reasons. * * * ## BioDeepTime v0.6 [2023-01-17] DOI ### Added - The Geobiodiversity Database - the Fenxiang section ### Changed - moved the coccolith data to "Direct uploads" ### Deleted - occurrenceTypeID column and occurenceType table ### Acknowledged - The two Neptune time series that have mixed taxonomy represent true data. * * * ## BioDeepTime v0.5.1 [2022-12-09] ### Changed - The sample age of the PBDB were in millions of years and not in years. Now they are in the correct unit. ## v0.5.0 [2022-11-21] ### Changed - Group entity is now unattached to the taxon, it is connected to time series entity * * * ## BioDeepTime v0.4.1 [2022-11-14] ### Added - MARBEN: ranks and opennomenclature * * * ## BioDeepTime v0.4.0 ### Added - Coccolithophore source dataset with 2 series - PBDB source dataset with 1 series ### Changed - Column name in denormalized table timeUnit -> timeOriginalUnit - Sedtraps data corrections: long species names, series name change ### To check, still - PBDB age model * * * ## BioDeepTime v0.3.0 [2022-10-08] ### Changed - omitted effortTargetReached and depthType - new versions of Neptune and Triton (no rounding) - Biotime references are added - ageNew is now called ageProc - added calibration for Radiocarbon ages - MARBEN ages added - omitted some neotoma samples that had no ages whatever - added bchron ages for neotoma - Triton abundances should be ok - SedTraps absence records are kept, occurrence's analyzedTaxon:NA, other taxon fields: 'No occurrence' ##### Neotoma - Some ages reach the endpoint of the calibration interval ##### BioTime - missing group, and taxonomy still, info still too incomplete - there are two samples with dates from Sept 31 - these are corrected to Sept 30 * * * ## BioDeepTime v0.2.1 [2022-10-04]