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Merge pull request #6 from Persdre/pr/5
Pr/5
2 parents 5e7ec91 + dfde296 commit 59c3b6a

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‎unsolved-exercises/00-tutorial.ipynb

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"FlyMine Beta<br/>\n",
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"XenMine"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Now that we have the mines, we can use `getInfo(mine)` to fetch all the information about a particular mine ie its description, version, organisms associated etc. Suppose we want to know more about flymine, here's what we do: "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"registry.getInfo(\"flymine\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Description: An integrated database for Drosophila genomics<br/>\n",
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"URL: http://www.flymine.org/flymine<br/>\n",
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"API Version: 25<br/>\n",
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"Release Version: 45.1 2017 August<br/>\n",
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"InterMine Version: 1.8.5<br/>\n",
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"Organisms: <br/>\n",
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"D. melanogaster<br/>\n",
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"Neighbours: <br/>\n",
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"MODs<br/>\n"
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]
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},
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Now that we have the mines, we can use `getInfo(mine)` to fetch all the information about a particular mine ie its description, version, organisms associated etc. Suppose we want to know more about flymine, here's what we do: "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"registry.getInfo(\"flymine\")"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"Description: An integrated database for Drosophila genomics<br/>\n",
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"URL: http://www.flymine.org/flymine<br/>\n",
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"API Version: 25<br/>\n",
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"Release Version: 45.1 2017 August<br/>\n",
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"InterMine Version: 1.8.5<br/>\n",
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"Organisms: <br/>\n",
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"D. melanogaster<br/>\n",
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"Neighbours: <br/>\n",
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"MODs<br/>\n"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/01-tutorial.ipynb

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"# 1. Import the intermine.webservice module\n",
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"from intermine.webservice import Service\n",
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"# 2. Instantiate a Service object. You can use \n",
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"# FlyMine's web service url: \"http://www.flymine.org/flymine/service\"\n",
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"# FlyMine's web service url: \"https://www.flymine.org/flymine/service\"\n",
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"# Or your favourite intermine.... \n",
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"# Syntax: service = Service(some_url)"
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]
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.4"
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/02-tutorial.ipynb

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"metadata": {},
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"outputs": [],
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"source": [
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"query=service.new_query(\"Organism\") "
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]
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},
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.4"
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/03-tutorial.ipynb

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"metadata": {},
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"outputs": [],
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"source": [
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"query=service.new_query(\"Gene\") "
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]
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},
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/04-tutorial.ipynb

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},
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"outputs": [],
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"source": [
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"query=service.new_query(\"Gene\")"
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]
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},
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/05-tutorial.ipynb

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"outputs": [],
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"source": [
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"from intermine.webservice import Service\n",
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"query=service.new_query(\"Gene\")\n",
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"query.select(\"publications.*\")\n",
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"query.add_constraint(\"Gene\",\"LOOKUP\",\"zen\",extra_value=\"D. melanogaster\")"
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/06-tutorial.ipynb

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"source": [
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"#Query setup\n",
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"from intermine.webservice import Service\n",
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"query=service.new_query()\n",
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"query.add_views(\"RNASeqResult.expressionScore RNASeqResult.expressionLevel RNASeqResult.gene.symbol\")"
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]
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 2
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/07-tutorial.ipynb

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"outputs": [],
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"source": [
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"from intermine.webservice import Service\n",
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"service = Service(\"www.flymine.org/flymine/service\")\n",
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"service = Service(\"https://www.flymine.org/flymine/service\")\n",
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"template=service.get_template('All_Genes_In_Organism_To_Publications')"
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]
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},
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/08-tutorial.ipynb

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"outputs": [],
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"source": [
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"#Update this line with your username, password, and change the url of the InterMine if needed.\n",
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"service=Service(\"www.flymine.org/flymine/service\",username=\"Enter username\",password=\"Enter password\")"
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"service=Service(\"https://www.flymine.org/flymine/service\",username=\"Enter username\",password=\"Enter password\")"
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]
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},
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{
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

‎unsolved-exercises/09-tutorial.ipynb

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"metadata": {},
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"outputs": [],
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"source": [
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"#service=Service(\"www.flymine.org/flymine/service\",username=\"Enter username\",password=\"Enter password\")"
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"#service=Service(\"https://www.flymine.org/flymine/service\",username=\"Enter username\",password=\"Enter password\")"
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]
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},
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{
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"metadata": {
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"anaconda-cloud": {},
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"kernelspec": {
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"display_name": "Python 2",
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"display_name": "Python 3",
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"language": "python",
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"name": "python2"
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython2",
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"version": "2.7.14"
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"pygments_lexer": "ipython3",
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"version": "3.7.4"
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}
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},
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"nbformat": 4,

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