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## gb.asc

      
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                GenBank specimen
              
          
Simple case of specimen and sequence both in GBIF


## zsm.asc

      
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                GenBank, BOLD, GBIF (ZSM iBOL)
              
          
GenBank, BOLD, GBIF (ZSM iBOL)


// GBIF occurrence


## permissions.txt
When copying MySQL database files (i.e. the binary files in /usr/local/mysql/data ) to a new machine we need to set permissions.

For  the database "db" we do the following:

sudo chown -R _mysql db
sudo chgrp -R _mysql db
sudo chmod -R 644 db
sudo chmod 755 db

## TTU Mammals 84773.csv
"Catalog# (TTU-M)","TK#","Genus","Species","Country","State","County","Collection Date","Tissues Available","Preparator"
"84773","104001","ARTIBEUS","OBSCURUS","ECUADOR","PASTAZA DISTRICT","---","7/19/2001","Yes","HAYNIE, M L"
"Subspecies: ---Specific Locality: 5 KM E PUYO, SAFARI HOSTERIA PARKElevation: ---Zone: 18Easting: 166624Northing: 9840350Latitude: ---Longitude: ---Collector: BAKER, R J ET ALPreparation Type: SBSex: FEMALEAssociated Sequences: ---Specimen#: ---Prep#: 157Prep Date: 7/19/2001Total Length (mm): 100Tail Length (mm): 0Foot Length (mm): 11Ear Length (mm): 12Weight (g): 14.9Tail Broken: NoTragus Length (mm): 0Forearm Length (mm): 0Reproductive Notes: ---Age: ADULT"

## occurrence.geojson

      
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                Museu Paraense Emilio Goeldi - Ornithology Collection GeoJSON for first 1000 records after lat/long divided by 10000000, see issue http://dev.gbif.org/issues/browse/POR-2649
              
          
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## index.html
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<html>
	<head>
		<title>www.boldsystems.org [8]</title>
		<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
		<meta http-equiv="pragma" content="no-cache">
		<style>
			body { margin:0; padding:0; }
		</style>
	</head>

## 576129791759384576.json
{
    "created_at": "Thu Mar 12 21:17:00 +0000 2015",
    "id": 576129791759384600,
    "id_str": "576129791759384576",
    "text": "#myGBIF (via web client)",
    "source": "<a href=\"http://twitter.com\" rel=\"nofollow\">Twitter Web Client</a>",
    "truncated": false,
    "in_reply_to_status_id": null,
    "in_reply_to_status_id_str": null,
    "in_reply_to_user_id": null,

## traits.html
<html>
	<head>
		<title>CouchDB-like view of EOL Trait data</title>
		<meta charset="UTF-8"/>
		<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
	</head>
<body>
<h1>CouchDB-like view of EOL Trait data</h1>
<p>API call like this: http://eol.org/api/traits/26374</p>
<div id="output"></div>

## bold.txt
BOLD has a (hidden) API to retrieve a Newick tree for a BIN. For example on the page http://www.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAD8242 we see an SVG tree. Under the hood this is called by: http://www.boldsystems.org/index.php/Public_Ajax_BINTree?clusterguid=BOLD:AAD8242&clusteruri=BOLD:AAD8242&clustername=BIN38242&clusterid=1738567

It's not clear where the "clusterid" comes from, but without it the API call fails.

## simple.sql
SELECT
IFNULL(id, ""),
IFNULL(cluster_id, ""),
IFNULL(nameComplete, ""),
IFNULL(taxonAuthor, ""),
IFNULL(`group`, ""),
IFNULL(publication, "")
INTO OUTFILE "/tmp/markus.tsv"
FIELDS TERMINATED BY "\t" ENCLOSED BY "" ESCAPED BY ""
LINES TERMINATED BY "\n"
	When copying MySQL database files (i.e. the binary files in /usr/local/mysql/data ) to a new machine we need to set permissions.

	For the database "db" we do the following:

	sudo chown -R _mysql db
	sudo chgrp -R _mysql db
	sudo chmod -R 644 db
	sudo chmod 755 db
	"Catalog# (TTU-M)","TK#","Genus","Species","Country","State","County","Collection Date","Tissues Available","Preparator"
	"84773","104001","ARTIBEUS","OBSCURUS","ECUADOR","PASTAZA DISTRICT","---","7/19/2001","Yes","HAYNIE, M L"
	"Subspecies: ---Specific Locality: 5 KM E PUYO, SAFARI HOSTERIA PARKElevation: ---Zone: 18Easting: 166624Northing: 9840350Latitude: ---Longitude: ---Collector: BAKER, R J ET ALPreparation Type: SBSex: FEMALEAssociated Sequences: ---Specimen#: ---Prep#: 157Prep Date: 7/19/2001Total Length (mm): 100Tail Length (mm): 0Foot Length (mm): 11Ear Length (mm): 12Weight (g): 14.9Tail Broken: NoTragus Length (mm): 0Forearm Length (mm): 0Reproductive Notes: ---Age: ADULT"
	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
	<html>
	<head>
	<title>www.boldsystems.org [8]</title>
	<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
	<meta http-equiv="pragma" content="no-cache">
	<style>
	body { margin:0; padding:0; }
	</style>
	</head>
	{
	"created_at": "Thu Mar 12 21:17:00 +0000 2015",
	"id": 576129791759384600,
	"id_str": "576129791759384576",
	"text": "#myGBIF (via web client)",
	"source": "<a href=\"http://twitter.com\" rel=\"nofollow\">Twitter Web Client</a>",
	"truncated": false,
	"in_reply_to_status_id": null,
	"in_reply_to_status_id_str": null,
	"in_reply_to_user_id": null,
	<html>
	<head>
	<title>CouchDB-like view of EOL Trait data</title>
	<meta charset="UTF-8"/>
	<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.2/jquery.min.js"></script>
	</head>
	<body>
	<h1>CouchDB-like view of EOL Trait data</h1>
	<p>API call like this: http://eol.org/api/traits/26374</p>
	<div id="output"></div>
	BOLD has a (hidden) API to retrieve a Newick tree for a BIN. For example on the page http://www.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri=BOLD:AAD8242 we see an SVG tree. Under the hood this is called by: http://www.boldsystems.org/index.php/Public_Ajax_BINTree?clusterguid=BOLD:AAD8242&clusteruri=BOLD:AAD8242&clustername=BIN38242&clusterid=1738567

	It's not clear where the "clusterid" comes from, but without it the API call fails.
	SELECT
	IFNULL(id, ""),
	IFNULL(cluster_id, ""),
	IFNULL(nameComplete, ""),
	IFNULL(taxonAuthor, ""),
	IFNULL(`group`, ""),
	IFNULL(publication, "")
	INTO OUTFILE "/tmp/markus.tsv"
	FIELDS TERMINATED BY "\t" ENCLOSED BY "" ESCAPED BY ""
	LINES TERMINATED BY "\n"