pybis demo.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Working with pybis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "········\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'vermeul-190613105017193x7338CBACCD9B0721D96EA8D19C3C3965'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pybis import Openbis\n",
    "o = Openbis(url='https://openbis-tst.ethz.ch', verify_certificates=False)\n",
    "import getpass\n",
    "password = getpass.getpass()\n",
    "\n",
    "o.login('vermeul',password, save_token=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>downloadUrl</th>\n",
       "      <th>remoteUrl</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DSS1</td>\n",
       "      <td>https://openbis-tst.ethz.ch:443</td>\n",
       "      <td>http://127.0.0.1:8081</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   code                      downloadUrl              remoteUrl\n",
       "0  DSS1  https://openbis-tst.ethz.ch:443  http://127.0.0.1:8081"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_datastores()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## connect to openBIS\n",
    "(using stored session token ~/.pybis/localhost.token)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'admin-190322224519031x6CD252246FDAD84555B20A030E8F60F8'"
      ]
     },
     "execution_count": 1,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pybis import Openbis\n",
    "o = Openbis(url='https://localhost:8443', verify_certificates=False)\n",
    "o.token"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'admin-190322225222678x9B6C922E404DB51F1C50A1B9DDFF371B'"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.login('admin', 'changeit', save_token=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{\"@type\": \"as.dto.common.search.SearchResult\", \"@id\": 1, \"objects\": [], \"totalCount\": 4}\n"
     ]
    },
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>permId</th>\n",
       "      <th>experiment</th>\n",
       "      <th>sample_type</th>\n",
       "      <th>registrator</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modifier</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "identifier    permId    experiment    sample_type    registrator    registrationDate    modifier    modificationDate\n",
       "------------  --------  ------------  -------------  -------------  ------------------  ----------  ------------------"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_samples(start_with=1, count=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "check if session is still active:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "False"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.is_session_active()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "login with a password if the token is no longer valid - and store the token"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "········\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'admin-190318124026896x8877AAC2A7790C251D8AE8A34D40FF1E'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pybis import Openbis\n",
    "o = Openbis('https://localhost:8443', verify_certificates=False)\n",
    "\n",
    "import getpass\n",
    "password = getpass.getpass()\n",
    "\n",
    "o.login('admin',password, save_token=True)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "you can connect to another openBIS instance if you like to:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "········\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "'vermeul-170213105248365xBB06092567F9EE09864C78CDBDB14CA9'"
      ]
     },
     "execution_count": 82,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from pybis import Openbis\n",
    "import getpass\n",
    "o2 = Openbis('https://sprint-openbis.ethz.ch:8443', verify_certificates=False)\n",
    "password = getpass.getpass()\n",
    "o2.login('vermeul',password)\n",
    "o2.token"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "disconnnect (or rather: make the session key invalid):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "o2.logout()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## get general information about openBIS"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Data Store Servers (DSS)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>downloadUrl</th>\n",
       "      <th>hostUrl</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DSS1</td>\n",
       "      <td>https://localhost:8444/datastore_server</td>\n",
       "      <td>https://localhost:8444</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   code                              downloadUrl                 hostUrl\n",
       "0  DSS1  https://localhost:8444/datastore_server  https://localhost:8444"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_datastores()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "list all available spaces:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>description</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ANOTHER_SPACE_NAME</td>\n",
       "      <td>another space description</td>\n",
       "      <td>2016-07-15 02:54:45</td>\n",
       "      <td>2016-07-15 02:54:45</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MATERIALS</td>\n",
       "      <td>None</td>\n",
       "      <td>2016-06-24 11:47:52</td>\n",
       "      <td>2016-06-24 11:47:52</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>METHODS</td>\n",
       "      <td>None</td>\n",
       "      <td>2016-06-24 11:47:53</td>\n",
       "      <td>2016-06-24 11:47:53</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MY_NEW_SPACE</td>\n",
       "      <td>this is yet another space</td>\n",
       "      <td>2016-07-15 03:02:14</td>\n",
       "      <td>2016-07-15 03:02:14</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>VERMEUL</td>\n",
       "      <td>Space for user vermeul</td>\n",
       "      <td>2016-06-24 11:50:48</td>\n",
       "      <td>2016-06-24 11:50:48</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f7ff39e4fd0>"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_spaces()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>attribute</th>\n",
       "                <th>value</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>code</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>permId</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>description</td> <td>this is yet another space</td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2016-07-15 03:02:14</td> </tr><tr> <td>modificationDate</td> <td>2016-07-15 03:02:14</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Space at 0x7f7ff5194898>"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sp = o.get_space('my_new_space')\n",
    "# another way: get space number 3 from the list above.\n",
    "# sp = o.get_spaces()[3]\n",
    "# sp = o.get_spaces()['MY_NEW_SPACE']\n",
    "sp"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "list all the projects within that space"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>permId</th>\n",
       "      <th>leader</th>\n",
       "      <th>registrator</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modifier</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td>\n",
       "      <td>20160926234755430-363</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-09-26 23:47:55</td>\n",
       "      <td>admin</td>\n",
       "      <td>2017-01-20 23:57:45</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f7ff39e8940>"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sp.get_projects()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "get details of the first project in this list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>attribute</th>\n",
       "                <th>value</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>code</td> <td>VERMEUL_PROJECT</td> </tr><tr> <td>description</td> <td>my first project in my space...</td> </tr><tr> <td>permId</td> <td>20160926234755430-363</td> </tr><tr> <td>identifier</td> <td>/MY_NEW_SPACE/VERMEUL_PROJECT</td> </tr><tr> <td>space</td> <td>MY_NEW_SPACE</td> </tr><tr> <td>leader</td> <td></td> </tr><tr> <td>registrator</td> <td>vermeul</td> </tr><tr> <td>registrationDate</td> <td>2016-09-26 23:47:55</td> </tr><tr> <td>modifier</td> <td>admin</td> </tr><tr> <td>modificationDate</td> <td>2017-01-20 23:57:45</td> </tr><tr><td>attachments</td><td>pybis.pdf</td></tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.pybis.Project at 0x7f6a2776dbe0>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pr = sp.get_projects()[0]\n",
    "# this works too:\n",
    "# pr = sp.get_projects()['/MY_NEW_SPACE/VERMEUL_PROJECT']\n",
    "pr"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**TAB completion**: list all possible attributes and methods by hitting the TAB key"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "# try it: put the cursor after the dot and press TAB\n",
    "pr."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Fetch the experiments that belong to a project"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [],
   "source": [
    "pr = o.get_project('/MY_NEW_SPACE/VERMEUL_PROJECT')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>permId</th>\n",
       "      <th>project</th>\n",
       "      <th>type</th>\n",
       "      <th>registrator</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modifier</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW</td>\n",
       "      <td>20170127005816666-430</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-27 00:58:17</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-27 00:58:17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
       "      <td>20160924020719018-358</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-09-24 02:07:19</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-09 00:05:43</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
       "      <td>20161121013609807-402</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-11-21 01:36:10</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-20 23:41:42</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "0\t/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW\n",
       "1\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
       "2\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT"
      ]
     },
     "execution_count": 88,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exs = pr.get_experiments()\n",
    "exs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "... using a different approach"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>identifier</th>\n",
       "      <th>permId</th>\n",
       "      <th>project</th>\n",
       "      <th>type</th>\n",
       "      <th>registrator</th>\n",
       "      <th>registrationDate</th>\n",
       "      <th>modifier</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW</td>\n",
       "      <td>20170127005816666-430</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-27 00:58:17</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-27 00:58:17</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4</td>\n",
       "      <td>20160924020719018-358</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-09-24 02:07:19</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-09 00:05:43</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPER...</td>\n",
       "      <td>20161121013609807-402</td>\n",
       "      <td>VERMEUL_PROJECT</td>\n",
       "      <td>None</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2016-11-21 01:36:10</td>\n",
       "      <td>vermeul</td>\n",
       "      <td>2017-01-20 23:41:42</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "0\t/MY_NEW_SPACE/VERMEUL_PROJECT/EXP_NEW\n",
       "1\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_EXPERIMENT4\n",
       "2\t/MY_NEW_SPACE/VERMEUL_PROJECT/MY_SPECIAL_EXPERIMENT"
      ]
     },
     "execution_count": 90,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_experiments(project='/MY_NEW_SPACE/VERMEUL_PROJECT')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "**get vocabulary terms**"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "\n",
       "            <table border=\"1\" class=\"dataframe\">\n",
       "            <thead>\n",
       "                <tr style=\"text-align: right;\">\n",
       "                <th>vocabulary term</th>\n",
       "                <th>label</th>\n",
       "                <th>description</th>\n",
       "                <th>vocabulary</th>\n",
       "                </tr>\n",
       "            </thead>\n",
       "            <tbody>\n",
       "        <tr> <td>PBLUESCRIPT_II_KS_PLUS</td> <td>pBluescript II KS +</td> <td>Commercial vector for cloning in bacteria (Stratagene)</td> <td>BACKBONE</td> </tr><tr> <td>PSPPOLY_A</td> <td>pSPpoly(A)</td> <td>Standard cloning vector. It can be used for in vitro trascription from SP6 promoter. It contains a poly(A) to generate poly(A)+ transcripts in vitro (Promega)</td> <td>BACKBONE</td> </tr><tr> <td>PRS30Y</td> <td>pRS30y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS31Y</td> <td>pRS31y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1989</td> <td>BACKBONE</td> </tr><tr> <td>PRS40Y</td> <td>pRS40y</td> <td>Integrative yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS41Y</td> <td>pRS41y</td> <td>Centromeric yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>PRS42Y</td> <td>pRS42y</td> <td>2-micron-based yeast shuttle vector from Sikorski et al, 1992</td> <td>BACKBONE</td> </tr><tr> <td>UNKNOWN</td> <td>unknown</td> <td>unknown vector</td> <td>BACKBONE</td> </tr><tr> <td>PGEX4T1</td> <td>pGEX4T1</td> <td>Vector for bacterial expression</td> <td>BACKBONE</td> </tr>\n",
       "            </tbody>\n",
       "            </table>\n",
       "        "
      ],
      "text/plain": [
       "<pybis.masterdata.Vocabulary at 0x7f3140fafeb8>"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x = o.get_terms('Backbone')\n",
    "x"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## get information about general types"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "OpenBIS categorizes some of its entities in «types»:\n",
    "\n",
    "* sample type\n",
    "* experiment type\n",
    "* material type\n",
    "* dataset type\n",
    "\n",
    "The types define the collection of **properties** that can be later assigned to a sample, experiment or dataset."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>description</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DEFAULT_EXPERIMENT</td>\n",
       "      <td>Default Experiment</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>MATERIALS</td>\n",
       "      <td>Folder used to organize samples in the Invento...</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>METHODS</td>\n",
       "      <td>Folder used to organize samples in the Invento...</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>BOARDS</td>\n",
       "      <td>Folder used to organize boards</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>UNKNOWN</td>\n",
       "      <td>Unknown</td>\n",
       "      <td>2016-06-24 10:47:01</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "<pybis.pybis.Things at 0x7f7ff3996a20>"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "o.get_experiment_types()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>code</th>\n",
       "      <th>description</th>\n",
       "      <th>generatedCodePrefix</th>\n",
       "      <th>modificationDate</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ANTIBODY</td>\n",
       "      <td></td>\n",
       "      <td>ANT</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CHEMICAL</td>\n",
       "      <td></td>\n",
       "      <td>CHE</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ENZYME</td>\n",
       "      <td></td>\n",
       "      <td>ENZ</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>MEDIA</td>\n",
       "      <td></td>\n",
       "      <td>MED</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SOLUTION_BUFFER</td>\n",
       "      <td></td>\n",
       "      <td>SOL</td>\n",
       "      <td>2016-06-24 10:48:02</td>\n",
       "    </tr>\n",
       "    <tr>\n",