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Standardizing Marine Biological Data Working Group - An open community to facilitate the mobilization of biological data to OBIS.
https://ioos.github.io/bio_data_guide/
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[dataset]: eDNA data (2018) from Banggai Island, Banggai MPA, Central Sulawesi, Indonesia #203

Open abigail2105 opened 9 months ago

abigail2105 commented 9 months ago

Contact details

abigail@pasca.unhas.ac.id

Dataset Title

Banggai eDNA 2018

Describe your dataset and any specific challenges or blockers you have or anticipate.

This dataset contains eDNA data from four sites around Banggai Island in the Banggai Archipelago, Central Sulawesi, Indonesia under a collaboration between Hasanuddin University in Makassar, Indonesia (UNHAS) and UCLA in 2018.

The sites are within the Banggai MPA, established formally in 2018. The water samples were collected using 1 litre infusion bags and filtered by gravity through Sterivex filtres with three replicates per site.

DNA was extracted at BIONESIA in Denpasar, Bali, Indonesia and the remaining processes were conducted at the Barber Lab, University of California Los Angeles (UCLA) under a partnership between Hasanuddin University in Makassar, Indonesia (UNHAS) and UCLA. Three primers were used: MiFISH teleost and elasmobranch (both performed well), and a COI primer (problems, no usable data obtained). Sequencing was performed on an Illumina MiSeq. The sequences were processed using the Anacapa pipeline.

The data we wish to submit are the 12S rRNA sequences of teleosts and elasmobranchs. Some of the data have been published (Moore A. M., Jompa J., Tassakka A. C. M. A. R., Yasir I., Ndobe S., Umar W., Gold Z., Barber P. H., 2021 Sharks and rays (Chondrichthyes) around Banggai Island, Banggai MPA, Indonesia: biodiversity data from an environmental DNA pilot study. AACL Bioflux 14(2):725-745. http://www.bioflux.com.ro/docs/2021.725-745.pdf). We also have two articles currently under consideration for publication and two in preparation.

This would be my first submission to OBIS, and as far as I am aware the first submission from my institution to OBIS. I am too inexperienced to really know where challenges or blockers are likely to occur. However, one challenge I anticipate is deciding what to include in (or exclude from) the dataset; another is how to address some taxonomic issues.

Info about "raw" Data Files.

The raw data are in an excel file from the Anacapa pipeline.

github-actions[bot] commented 6 months ago

Thank you for identifying this dataset for mobilization. The workshop hosts wanted to check in. Is there anything you need help with in order to mobilize this dataset to OBIS? If you would like assistance from an OBIS node you can find node contacts listed here.