Jong

#[04/19 - 04/25] Updating Slides + Functions

• Waiting for Roy in his front-end database UI to make modifications
  • Currently missing scientificname, count, and database for idigbio_commonname_taxon function, but Roy said to wait
• Updated slides accordingly from the link from gitter: BIDS PPT Slides

#[04/12 - 04/18] Separate function for CommonName and Taxonomy

• Created a new function that returned commonname and taxonomy based on the scientific name query
• Also updated search_idigbio_location function so that location could be an optional parameter, with default = ""

#[04/05 - 04/11] Country Location Search

• Integrated country search function as well
• Redundant code between the two search functions (one with, one without) so combining together
• Next week: Integrate search function into one, get common name
• Look into if cases matter or not in search query fields

#[03/30 - 04/04] Occurrence Count

• New branch jong_gh created
• Occurrence count added when specie searched
• Testing country occurrence count as well in testing folder idigbioAPI_test.js

#[03/09-03/14] New Databases

• Note: Is this similar to what we are trying to do? http://www.catalogueoflife.org/
• IUCN Red List: http://apiv3.iucnredlist.org/api/v3/docs a comprehensive biodiversity database, but also shows whether species is endangered or not. Waiting for API Key at the moment, but used a sample on listed on website.
• BOLD Systems API: Problem - Returns TSV or XML file; so convert TSV to JSON using another function; still working in progress
• http://www.programmableweb.com/news/101-biology-apis-biocatalogue-biogrid-and-synergizer/2013/10/22 A bunch of biological APIs (can't determine whether one is better or not).

#[03/02 - 03/08] iDigBio Specie exists dictionary

• Used "mode" function created before to return most common scientific name and taxon if specie exists
• Modified it to be asychronous calls

#[02/24 - 03/01] iDigBio General Data

• Created General data object based on all observations resulting from query.
• Implemented new functions (mode, and find_unique) to find most common scientific name, and aggregate all common names and countries.
• Could use functions for other APIs as well
• General Data could now be used to be displayed on the webpage, instead of all observations.

#[02/16 - 02/23] iDigBio Data Scraping and Cleaning

• Used POST instead of GET method (returned more/better results).
• Created iDigBio.js file that contains code to extract data from iDigBio API, and what data we are extracting
• New index.html file that uses iDigBio.js as src script
• Small problem: Could not use colon (:) in trying to get source because the source code was data.items[i].data.dcterms:bibliographicCitation but colons weren't allowed in JS
• Could possibly use iDigBio Download API (but looks like it's still primitive)

Important links:
iDigBio Search API Home Page
Index Fields
iDigBio Download API

#[02/09 - 02/16] Preliminary Database Research for Reptile Biodiversity Data

##1. Global Biodiversity Information Facility (GBIF) Preliminary Search Query "Reptiles"

GBIF is one of the biggest and well-known database of all species, including Reptiles. A preliminary search on "Reptiles" displayed 44,726 results, and the search displayed in this order, for each result:

Then on the side, it indicated ways to refine the search, including limiting the search to species, order, family, etc. In addition, it had options to span different databases as well, not limited to the GBIF database. Other categories could be checklisted as well, including habitat, name type, extinct/not extinct, status, etc.
Upon clicking on the result, it gave much more detailed information, including sources as well. An interesting visual aspect of the search was that a global map in which the specie existed was displayed, varying in the quantity and color of dots based on the number of that specific specie living there.

##2. The Reptile Database Official Website
Although at first sight the website interface and design isn't the most pleasing, it does have a remarkable amount of history, reaching its 20th anniversary since its inception (there is a Wikipedia page for it!). A very general search query "snake" displays results in the form of # of results, and specie name followed by (first publication of discovery of species). The database isn't as thorough in information as GBIF, as displayed below:

There are some information, including the location, common names, type, and lots of references. One interesting aspect of this database is that it tries to display pictures if possible of each species. The data can also be downloaded in Excel format, or tab-delimited format.

##3. Snake Database http://snakedatabase.org/pages/search.php My search for a generalized reptile-specific databases proved to be difficult; however, instead I found database in regards to specific types of reptiles, one of which was the Snake Database. This website differs from other databases in that it requires the user to make the search through five categories: Superfamily, Family, Subfamily, Genus, and Species. The categories narrow down depending on the user's input from the previous category. The information the website provides is a little more user friendly, including information about first aid, bite, behavior, medical importance, etc, and does not seem like it is a database used for research purposes.

As the database is solely for learning about snakes, there are various other database that are specifically pertinent, including Snake Venom LD50 database, Venom Distribution, etc. Unfortunately there does not seem to be a way to download the dataset separately.

##4. EMYSystem http://emys.geo.orst.edu/ The EMYSystem is an information repository supporting global turtle conservation. Its goal is to collect and provide current and historical data about turtle locations, and to help maintain the variety of turtles as part of the world's biodiversity. Similarly to the snake database, the EMYSystem database solely focuses on turtles, and has its turtle data on the "World Turtle Database". Unfortunately it does not contain much information about the turtles themselves.

##5. Other databases The rest of the databases follow the structure of GBIF, which is a generalized database which does still contain information about Reptiles. They aren't necessarily specialized to reptiles, and such database include: Species+, Encyclopedia of Life (EoL), among many others. Species+ enables the user to download the data set by inputting categories that narrows down the search, but requires the user to put in the actual taxonomic term to search (for ex: reptilia, instead of reptile). Encyclopedia of Life seems more media-based, with lots of photos, community-based summaries, forums, etc. However, it does not seem to have much information about reptiles.