"print(\"L\\'identifiant du corpus est : %s\" % corpus_id)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# To get all the documents:\n",
"docs = documents(corpus_id)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the title of the first document \n",
"# [0] indicates the index of the first document\n",
"docs[0].hyperdata['title']"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"\"The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.\""
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the abstract of the first document (0)\n",
"docs[0].hyperdata['abstract']"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan, Tin Wee Tan'"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the authors of the first document (0)\n",
"docs[0].hyperdata['authors']"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'BMC bioinformatics'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the source of the first document (0)\n",
"docs[0].hyperdata['source']"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# If I want to count:\n",
"myChart = chart(docs, \"publication_year\")"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x7f48069c5208>"
"[clean_lang_inText('en', abstract) for abstract in [abstract0, abstract1]]\n",
"\n",
"# TODO update each document accordingly"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# TODO update all the abstract with That function"
]
},
{
"cell_type": "markdown",
"metadata": {
"deletable": true,
"editable": true
},
"source": [
"# Measures IMT Tools"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"ename": "ConnectionError",
"evalue": "HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/packages/urllib3/connection.py\u001b[0m in \u001b[0;36m_new_conn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 150\u001b[0m raise NewConnectionError(\n\u001b[0;32m--> 151\u001b[0;31m self, \"Failed to establish a new connection: %s\" % e)\n\u001b[0m\u001b[1;32m 152\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNewConnectionError\u001b[0m: <requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mMaxRetryError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;32m<ipython-input-16-b220cbbc8ecc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mscan_hal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"machine learning AND deep\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 584\u001b[0m \u001b[0;31m# Send the request\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 585\u001b[0;31m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0madapter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 586\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 587\u001b[0m \u001b[0;31m# Total elapsed time of the request (approximately)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mConnectionError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))"
"{'abstract': 'The purpose of this paper is to develop a new fuzzy dynamic programming approach for solving hybrid multiobjective multistage decision-making problems. We first present a methodology of fuzzy evaluation and fuzzy optimization for hybrid multiobjective systems, in which the qualitative and quantitative objectives are synthetically considered. The qualitative objectives are evaluated by decision-makers with linguistic variables and the quantitative objectives are converted into proper dimensionless indices. After getting the marginal evaluations for each objective, a new aggregation method based on the principle of fuzzy pattern recognition is developed to get a global evaluation for all objectives. With the global evaluation obtained, a fuzzy optimization process is performed. Then we present a dynamic optimization algorithm by incorporating the fuzzy optimization process with the conventional dynamic programming technique to solve hybrid multiobjective multistage decision-making problems. A characteristic feature of the approach proposed is that various objectives are synthetically considered by the fuzzy systematic technique instead of the frequently employed weighted average method. Finally, an illustrative example is also given to clarify the developed approach and to demonstrate its effectiveness.',\n",
" 'authors': 'Lushu Li, K.K. Lai',\n",
" 'authorsRAW': [{'affiliations': ['Faculty of Administration, University of New Brunswick, Fredericton, N.B., Canada',\n",
" 'Corresponding author'],\n",
" 'name': 'Lushu Li'},\n",
" {'affiliations': ['Department of Management Science, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong'],\n",
"print(\"L\\'identifiant du corpus est : %s\" % corpus_id)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# To get all the documents:\n",
"docs = documents(corpus_id)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference.'"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the title of the first document \n",
"# [0] indicates the index of the first document\n",
"docs[0].hyperdata['title']"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"\"The 2011 International Conference on Bioinformatics (InCoB) conference, which is the annual scientific conference of the Asia-Pacific Bioinformatics Network (APBioNet), is hosted by Kuala Lumpur, Malaysia, is co-organized with the first ISCB-Asia conference of the International Society for Computational Biology (ISCB). InCoB and the sequencing of the human genome are both celebrating their tenth anniversaries and InCoB's goalposts for the next decade, implementing standards in bioinformatics and globally distributed computational networks, will be discussed and adopted at this conference. Of the 49 manuscripts (selected from 104 submissions) accepted to BMC Genomics and BMC Bioinformatics conference supplements, 24 are featured in this issue, covering software tools, genome/proteome analysis, systems biology (networks, pathways, bioimaging) and drug discovery and design.\""
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the abstract of the first document (0)\n",
"docs[0].hyperdata['abstract']"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan, Tin Wee Tan'"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the authors of the first document (0)\n",
"docs[0].hyperdata['authors']"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"'BMC bioinformatics'"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# To get the source of the first document (0)\n",
"docs[0].hyperdata['source']"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# If I want to count:\n",
"myChart = chart(docs, \"publication_year\")"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"data": {
"text/plain": [
"<matplotlib.axes._subplots.AxesSubplot at 0x7f48069c5208>"
"[clean_lang_inText('en', abstract) for abstract in [abstract0, abstract1]]\n",
"\n",
"# TODO update each document accordingly"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true,
"deletable": true,
"editable": true
},
"outputs": [],
"source": [
"# TODO update all the abstract with That function"
]
},
{
"cell_type": "markdown",
"metadata": {
"deletable": true,
"editable": true
},
"source": [
"# Measures IMT Tools"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {
"collapsed": false,
"deletable": true,
"editable": true
},
"outputs": [
{
"ename": "ConnectionError",
"evalue": "HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/packages/urllib3/connection.py\u001b[0m in \u001b[0;36m_new_conn\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 150\u001b[0m raise NewConnectionError(\n\u001b[0;32m--> 151\u001b[0;31m self, \"Failed to establish a new connection: %s\" % e)\n\u001b[0m\u001b[1;32m 152\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNewConnectionError\u001b[0m: <requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mMaxRetryError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;32m<ipython-input-16-b220cbbc8ecc>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mscan_hal\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"machine learning AND deep\"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/home/alexandre/local/logiciels/python/env/3.5_20170123/lib/python3.5/site-packages/requests/sessions.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, request, **kwargs)\u001b[0m\n\u001b[1;32m 583\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 584\u001b[0m \u001b[0;31m# Send the request\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 585\u001b[0;31m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0madapter\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m**\u001b[0m\u001b[0mkwargs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 586\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 587\u001b[0m \u001b[0;31m# Total elapsed time of the request (approximately)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mConnectionError\u001b[0m: HTTPSConnectionPool(host='api.archives-ouvertes.fr', port=443): Max retries exceeded with url: /search?wt=json&q=machine+learning+AND+deep&fl=+title_s%0A+++++++++++++++%2C+abstract_s%0A+++++++++++++++%2C+submittedDate_s%0A+++++++++++++++%2C+journalDate_s%0A+++++++++++++++%2C+authFullName_s%0A+++++++++++++++%2C+uri_s%0A+++++++++++++++%2C+isbn_s%0A+++++++++++++++%2C+issue_s%0A+++++++++++++++%2C+docType_s%0A+++++++++++++++%2C+journalPublisher_s%0A+++++++++++++&start=1&rows=10 (Caused by NewConnectionError('<requests.packages.urllib3.connection.VerifiedHTTPSConnection object at 0x7f48069d1f98>: Failed to establish a new connection: [Errno -3] Temporary failure in name resolution',))"
