Biodiversity databases

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.title[
# Biodiversity databases
]
.subtitle[
## Serrapilheira/ICTP-SAIFR Training Program in Quantitative Biology and Ecology
]
.author[
### Andrea Sánchez-Tapia & Sara Mortara
]
.date[
### 27 July 2022
]

---

## today

1. Biodiversity databases: basic concepts

2. DarwinCore standard

3. Biodiversity data cleaning

4. A workflow in R

---
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# 1. Biodiversity databases: basic concepts

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## Biodiversity data
### Museums, herbaria, collections

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<img src="./figs/mz_ictio.jpg" width="500" />
]

.pull-right[
<img src="./figs/herbarioRB.jpg" width="400" />
]

---
.pull-left[
## Who creates these data?

- Researchers: taxonomists, ecologists, field biologists
- Undergrad and grad school courses
- Amateur collectors, citizen science, using apps or not

]

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## Who uses them?

- Researchers
- Curators
- The overall community (e.g., bird watchers)

]

+ A __massive__ amount of data

+ New research areas from the analysis and synthesis of these data: Biogeography, macroecology

+ __However__: heterogeneous quality, inequality between countries and institutions

---

---
## Biodiversity databases

- [GBIF](https://www.gbif.org/) (Global Biodiversity Information Facility)

- Country-wise biodiversity information systems: 
    + 🇧🇷 [speciesLink](http://splink.cria.org.br/), Sistema de Informações sobre Biodiversidade Brasileira [SiBBr](https://www.sibbr.gov.br/)
    + 🇨🇴 Sistema de Información sobre Biodiversidad [SibColombia](https://biodiversidad.co/)
    + 🇲🇽 Sistema Nacional de Información sobre Biodiversidad [SNIB](https://snib.mx/)
    + 🇦🇷 Sistema de Información de Biodiversidad [SIB](https://sib.gob.ar/#!/)

- Countries that participate via ministries, agencies

- Other systems:

- Natureserve/ BISON in the USA
    - [iNaturalist](https://www.inaturalist.org/)

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## By taxonomic group

+ [World Flora Online](http://www.worldfloraonline.org/)

+ [Plants of the world](http://plantsoftheworldonline.org/)

+ [International Plant Name Index (IPNI)](https://www.ipni.org/)

+ [Fishbase](https://www.fishbase.in/)

+ [Mammal Diversity](https://www.mammaldiversity.org/)

---
## <img src="./figs/Ropensci.png" width="239" />

> Transforming science through open data, software & reproducibility

- R packages to make data available, data cleaning, APIs

- __Package peer-review__

- Packages related to biodiversity data retrieval, manipulation, and standardization: `finch`, `rgbif`, `taxize`, `taxview` ...

---
## Looking at GBIF data

Let's download the data of a tree species from South America *Myrsine coriacea* from the Primulaceae family.

```r
library(rgbif)
library(dplyr)
species <- "Myrsine coriacea"
occs <- occ_search(scientificName = species)
names(occs)
#glimpse(occs)
#names(occs$data)
```

Column names returned from gbif follow the DarwinCore standard (https://dwc.tdwg.org).

---
## Possible fields

+ Species (taxonomic information)

+ Locality, coordinates, geographic

+ Collector notes and species attributes, IUCN status

+ Collectors, determiners, and authors' names

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# 2.DarwinCore Standard

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## [DarwinCore](https://dwc.tdwg.org/)

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- goal: __facilitate the sharing of information about biological diversity__ by providing identifiers, labels, and definitions

- maintained by a working group, adopted globally by GBIF and most collections, constant evolution

- [_reference guide_](https://dwc.tdwg.org/terms/): `Taxon`, `Event`, `Identification`, `Location`

]

.pull.right[
<img src="./figs/darwin.jpeg" width="350" style="display: block; margin: auto;" />
]

---

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## Multi-file [DwC scheme](https://dwc.tdwg.org/)

+ a ZIP file with:

+ different data tables (__relational databases__)
  + description file (__XML__)
  + metadata files (__EML__ [Ecological Metadata Language](https://eml.ecoinformatics.org/))

+ __common columns__ for each table, `ID`

---

+ IPT is used to publish your data, __either in one single table__ or __extended__: species lists, field work samplings etc. Datasets are given a __permanent identifier and citation__

---
## <img src="./figs/IPT.png" width="599" />

> Brazil Flora G (2020): Brazilian Flora 2020 project - Projeto Flora do Brasil 2020. v393.274. Instituto de Pesquisas Jardim Botanico do Rio de Janeiro. Dataset/Checklist. doi:10.15468/1mtkaw URL: http://ipt.jbrj.gov.br/jbrj/

- 49.343 species

- 136.314 taxa

- Information about: distribution, habitat, endemism, references, synonyms

- IPT in `R`: package __finch__ ([Chamberlain 2020](https://CRAN.R-project.org/package=finch))

---
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# 3. Data cleaning

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## Primary data are not clean or updated

- Names and classifications change in time (synonyms):

- International Commission on Zoological Nomenclature ([ICZN](https://www.iczn.org/)),  International Code of Botanical Nomenclature, [International Association for Plant Taxonomy](https://www.iapt-taxon.org/icbn/main.htm) 
  
  - The names of places: __toponyms__, we need _gazetteers_
  
- Taxonomic identification errors, georreferencing, typographic/orthographic

- Missing coordinates or localities

- Imprecise coordinates, badly attributed

---

## Spatial error

[Yesson et al 2007](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2043490/)

---

## Zero latitude and longitude

[Yesson et al 2007](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2043490/)

---
## Taxonomic, nomenclatural erros

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+ Original vs. accepted name

- Different taxonomic concepts / backbones, premisses, measure units.

- New errors arising in processing and junction

- Duplicate data vs. _duplicatae_

]

.pull-right[
<img src="figs/paubrasil.png" width="450" style="display: block; margin: auto 0 auto auto;" />

]

---
## Data cleaning workflow

Check for

1. format
2. completeness
3. sense (dimensions, ranges)
4. outliers (geographic, temporary, environmental)

---
## Good practices:

+ Always flag 🚩 additions, corrections, __never modify__ original data

+ Document all steps -> reproducibility

+ Cite packages and data sources

---

## Know your shortfalls

> informed ignorance is a powerful research tool

---

## References

Chapman, A. D. (2005). Principles and methods of data cleaning. GBIF.

Hortal, J., de Bello, F., Diniz-Filho, J. A. F., Lewinsohn, T. M., Lobo, J. M., & Ladle, R. J. (2015). Seven shortfalls that beset large-scale knowledge of biodiversity. Annual Review of Ecology, Evolution, and Systematics, 46, 523-549.

Yesson, C., Brewer, P. W., Sutton, T., Caithness, N., Pahwa, J. S., Burgess, M., ... & Culham, A. (2007). How global is the global biodiversity information facility?. PloS one, 2(11), e1124.

Wieczorek, J., Bloom, D., Guralnick, R., Blum, S., Döring, M., Giovanni, R., ... & Vieglais, D. (2012). Darwin Core: an evolving community-developed biodiversity data standard. PloS one, 7(1), e29715.

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# ¡Thanks!

<center>
<svg viewBox="0 0 512 512" style="position:relative;display:inline-block;top:.1em;fill:#A70000;height:1em;" xmlns="http://www.w3.org/2000/svg">  <path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"></path></svg> [andreasancheztapia@gmail.com](mailto:andreasancheztapia@gmail.com) | [saramortara@gmail.com](mailto:saramortara@gmail.com)