apc-analysis.ipynb

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     "source": [
      "APC Analysis\n",
      "=====================\n",
      "\n",
      "Following the release of a range of datasets on APC payments on individual articles from the Wellcome Trust, Cambridge University, Queens University Belfast and the Austrian Research Foundation (FWF) there is an interest in how well the Open Article Gauge performs in determining the Open Access status of the articles both in terms of licensing and the question of whether the articles are in OA journals or in hybrid journals.\n",
      "\n",
      "This work builds on the crowdsourcing that was done on the original Wellcome Trust 2012/13 data [as described in this post](http://access.okfn.org/2014/04/01/wellcome-trust-apc-data-thank-you/). Initial data processing was carried out by loading the Excel files provided and converting them to csv files. In the case of the Cambridge file the first line of the original excel file was deleted before doing this to make it easier to handle.\n",
      "\n",
      "The original data files can be found within this repository in the /input_data folder as follows:\n",
      "\n",
      "* [Wellcome Trust 2012/13 data](https://github.com/cameronneylon/apcs/tree/master/input_data/wellcome/2012-13)\n",
      "* [Wellcome Trust 2010-12 data](https://github.com/cameronneylon/apcs/tree/master/input_data/wellcome/2010-12)\n",
      "* [Cambridge University 2013/14 data](https://github.com/cameronneylon/apcs/tree/master/input_data/cambridge)\n",
      "* [Queens University Belfast 2013/14 data](https://github.com/cameronneylon/apcs/tree/master/input_data/qub)\n",
      "* [Austrian Research Foundation (FWF)](https://github.com/cameronneylon/apcs/tree/master/input_data/fwf)"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Data organisation\n",
      "-----------------\n",
      "\n",
      "The intention is to create a concatenated output which includes the fields Data Source, Publisher, Article Title, Journal, DOI, Cost, Manually determined license, Manually determined status, OAG determined license, URL, License statement. This involves loading the files separately as there are differences between them. We will use csv files created from the Cambridge, QUB, FWF and Wellcome 2010-12 datasets and the crowdsourced data for the Wellcome 2012-13 datasets.\n",
      "\n",
      "###Obtaining Identifiers (DOIs, PMIDs, PMCIDs)###\n",
      "\n",
      "DOIs are quite complete for QUB, Cambridge and FWF sets but missing from the original Wellcome sets. The Wellcome data mainly contain PMCIDs but these are inconsistently formatted and not easy to process. It is more straightforward to use the Crossref search API to obtain DOIs than to attempt to parse the PMCIDs. This will also allow us to fill in missing DOIs from the crowdsourced Wellcome 2012/13 data.\n",
      "\n",
      "###Representation of status and licensing###\n",
      "\n",
      "The QUB and Cambridge datasets only contain the field 'Correct license?' determining whether the license can be determined to be CC BY. The FWF data only includes the field 'Open Access' presumably meaning free-to-read. The crowdsourced 2012/13 Wellcome data contains fairly consistently formatted license indicators but different ones to those generated by the OAG. In this case we wish to normalise to the set used by the OAG so will apply this to the QUB, Cambridge and 2012/13 Wellcome datasets to make them consistent with OAG representation."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "#Useful imports\n",
      "%load_ext autoreload\n",
      "%autoreload 2\n",
      "import requests\n",
      "import pyoag\n",
      "import csv\n",
      "import urllib\n",
      "import math\n",
      "import json\n",
      "\n",
      "# Set up our data container\n",
      "articles = []\n",
      "\n",
      "# Quick convenience method for loading the files\n",
      "def load_csv(path, fields, source):\n",
      "    list = []\n",
      "    with open(path, 'rU') as f:        \n",
      "        reader = csv.DictReader(f)\n",
      "        data = [line for line in reader]\n",
      "        #print reader.fieldnames\n",
      "        \n",
      "    for line in data:\n",
      "        article = {'source' : source}\n",
      "        for inputfield, outputfield in fields:\n",
      "            article[outputfield] = line.get(inputfield)\n",
      "        list.append(article)\n",
      "    \n",
      "    return list"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "The autoreload extension is already loaded. To reload it, use:\n",
        "  %reload_ext autoreload\n"
       ]
      }
     ],
     "prompt_number": 55
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Importing the Data\n",
      "-----------------------\n",
      "\n",
      "###Wellcome Trust###\n",
      "The crowdsourced data contains a wide range of columns. We only need a few of these. The earlier data has less columns and less clean information on publishers etc. There may be a need for normalising journal names and publishers at some point but we will start with what we have. "
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fields = [('Publisher', 'publisher'), \n",
      "          ('DOI', 'doi'), \n",
      "          ('Journal Title', 'journal'), \n",
      "          ('Article title', 'title'), \n",
      "          ('Cost', 'cost'),\n",
      "          ('CC licence type', 'manual_license'),\n",
      "          ('Hybrid or Pure', 'manual_status')]\n",
      "\n",
      "wellcome1213 = load_csv('input_data/wellcome/2012-13/Crowdsource-12-13.csv', fields, 'wellcome-12-13') \n",
      "articles.extend(wellcome1213)\n",
      "print wellcome1213[0:2]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[{'publisher': 'Elsevier (Cell Press)', 'doi': '0.1016/j.tins.2013.08.001', 'title': 'Cytoplasmic dynein heavy chain: the servant of many masters', 'journal': 'Trends in Neurosciences', 'source': 'wellcome-12-13', 'cost': '\\xa32,404.40', 'manual_license': '', 'manual_status': None}, {'publisher': 'Oxford University Press', 'doi': '0.1093/ije/dyt086', 'title': 'Cohort Profile: - A prospective cohort study of objective physical and cognitive capability and visual health in an ageing population of men and women in Norfolk (EPIC-Norfolk 3)', 'journal': 'International Journal of Epidemiology', 'source': 'wellcome-12-13', 'cost': '\\xa32,400.00', 'manual_license': '', 'manual_status': None}]\n"
       ]
      }
     ],
     "prompt_number": 56
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "For the two uncleaned data sets the situation is simpler but potentiall more messy. We will likely want to clean up publisher and journal names later. But there are less fields to deal with."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fields = [('Publisher', 'publisher'),  \n",
      "          ('Journal title', 'journal'), \n",
      "          ('Article title', 'title'), \n",
      "          ('COST (\\xa3)', 'cost')]\n",
      "\n",
      "wellcome1011 = load_csv('input_data/wellcome/2010-12/wellcome_apcs_10-11.csv', fields, 'wellcome-10-11')\n",
      "articles.extend(wellcome1011)\n",
      "print wellcome1011[0:2], '\\n'\n",
      "\n",
      "wellcome1112 = load_csv('input_data/wellcome/2010-12/wellcome_apcs_11-12.csv', fields, 'wellcome-11-12')\n",
      "articles.extend(wellcome1112)\n",
      "print wellcome1011[0:2]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[{'source': 'wellcome-10-11', 'journal': 'Journal of Immunology', 'title': 'IL-10 restricts activation-induced death of NK cells during acute murine cytomegalovirus infection', 'cost': '\\xa3678.27', 'publisher': 'American Association of Immunologists'}, {'source': 'wellcome-10-11', 'journal': 'ACS Chemical Biology', 'title': 'Hypoxia triggers major metabolic changes in AML cells without altering indomethacin-induced TCA cycle deregulation', 'cost': '\\xa31,250.00', 'publisher': 'American Chemical Society'}] \n",
        "\n",
        "[{'source': 'wellcome-10-11', 'journal': 'Journal of Immunology', 'title': 'IL-10 restricts activation-induced death of NK cells during acute murine cytomegalovirus infection', 'cost': '\\xa3678.27', 'publisher': 'American Association of Immunologists'}, {'source': 'wellcome-10-11', 'journal': 'ACS Chemical Biology', 'title': 'Hypoxia triggers major metabolic changes in AML cells without altering indomethacin-induced TCA cycle deregulation', 'cost': '\\xa31,250.00', 'publisher': 'American Chemical Society'}]"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 57
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###QUB and Cambridge###\n",
      "\n",
      "The QUB data is the simplest to grab. The Cambridge dataset uses a similar table but has been enhanced by including data both on the status of the article on publication and more recently. To deal with this I manually removed the first line of the csv file and changed some of the column headings to make these two files easy to load together. This means for the Cambridge set we are using the more up to date information on whether the article is OA and its license. \n",
      "\n",
      "In the case of the QUB dataset there are two columns for those articles where VAT was assessed and where it wasn't. This needs to be cleaned up into the single cost column."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fields = [('Publisher', 'publisher'),  \n",
      "          ('Journal', 'journal'), \n",
      "          ('Article', 'title'),\n",
      "          ('DOI', 'doi'),\n",
      "          ('Amount paid on APC (incl. VAT)', 'cost'),\n",
      "          ('Correct licence?', 'manual_license'),\n",
      "          ('Open Access?', 'manual_status')]\n",
      "\n",
      "cambridge = load_csv('input_data/cambridge/cambridge_apcs.csv', fields, 'cambridge-13-14')\n",
      "\n",
      "fields = [('Publisher', 'publisher'),  \n",
      "          ('Journal', 'journal'), \n",
      "          ('Article', 'title'),\n",
      "          ('DOI', 'doi'),\n",
      "          ('Amount paid on APC (VAT included)', 'cost'),\n",
      "          ('Amount paid on APC (VAT not included)', 'ex-vat'),\n",
      "          ('Correct licence?', 'manual_license'),\n",
      "          ('Open Access?', 'manual_status')]\n",
      "\n",
      "qub = load_csv('input_data/qub/qub_apcs.csv', fields, 'qub-13-14')\n",
      "print cambridge[0:2], '\\n'\n",
      "print qub[0:2]\n",
      "\n",
      "new = qub+cambridge\n",
      "for a in new:\n",
      "    if a.get('manual_license') == 'Y':\n",
      "        a['manual_license'] = 'cc-by'\n",
      "    if a.get('manual_status') == 'Y':\n",
      "        a['manual_status'] = 'free-to-read'\n",
      "    if a.get('ex-vat'):\n",
      "        a['cost'] = a.get('ex-vat')\n",
      "        del a['ex-vat']\n",
      "\n",
      "articles.extend(new)        "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[{'publisher': 'Elsevier', 'doi': '10.1016/j.marpetgeo.2013.11.005', 'title': 'Evidence for multiple Quaternary ice advances and fan development from the Amundsen Gulf cross-shelf trough and slope, Canadian Beaufort Sea margin', 'journal': 'Marine and Petroleum Geology', 'source': 'cambridge-13-14', 'cost': '\\xa31,893.38', 'manual_license': 'Y', 'manual_status': 'Y'}, {'publisher': 'Elsevier', 'doi': '10.1016/j.jcrysgro.2013.07.035', 'title': 'Surface morphology of homoepitaxial c-plane GaN: hillocks and ridges', 'journal': 'Journal of Crystal Growth', 'source': 'cambridge-13-14', 'cost': '\\xa31,730.22', 'manual_license': 'Y', 'manual_status': 'Y'}] \n",
        "\n",
        "[{'publisher': 'AIP', 'doi': '10.1063/1.4818888', 'ex-vat': '', 'title': 'Ion-acoustic supersolitons in plasmas with two-temperature electrons: Boltzmann and kappa distributions', 'journal': 'Physics of Plasmas', 'source': 'qub-13-14', 'cost': '\\xa31,581.50', 'manual_license': 'N', 'manual_status': 'Y'}, {'publisher': 'Biochemical Society', 'doi': '10.1042/BST20130088', 'ex-vat': '', 'title': 'Molecular mechanism and physiological role of active\\xd0deactive transition of mitochondrial complex I', 'journal': 'Biochemical Society Transactions', 'source': 'qub-13-14', 'cost': '\\xa31,800.00', 'manual_license': 'N', 'manual_status': 'N'}]\n"
       ]
      }
     ],
     "prompt_number": 58
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###Austrian Research Foundation###\n",
      "\n",
      "For the FWF we have an added complication that the dataset includes a large number of non-APC costs. Some of these are definitely publication costs and it is an interesting question whether they should be included. However for this analysis we are focussing only on explicit APCs so we will filter out the non-APC costs based on 'Cost type' column. We will also use this column to populate the 'manual_status' field."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fields = [('Publisher', 'publisher'),  \n",
      "          ('Journal title', 'journal'), \n",
      "          ('Article title', 'title'),\n",
      "          ('DOI/PMID', 'doi'),\n",
      "          ('Cost (\\xdb)', 'cost'),\n",
      "          ('Cost type', 'type'),\n",
      "          ('Open Access', 'manual_status')]\n",
      "\n",
      "fwf = load_csv('input_data/fwf/fwf_pubcosts.csv', fields, 'fwf-13')\n",
      "print fwf[0:2]\n",
      "\n",
      "apc = [a for a in fwf if ((a.get('type') == 'Hybrid Open Access') or (a.get('type') == 'Gold Open Access'))]\n",
      "for a in apc:\n",
      "    if a.get('manual_status') == 'OA':\n",
      "        if a.get('type') == 'Hybrid Open Access':\n",
      "            a['manual_status'] = 'hybrid'\n",
      "        if a.get('type') == 'Gold Open Access':\n",
      "            a['manual_status'] = 'pure'\n",
      "    del a['type']\n",
      "    \n",
      "articles.extend(apc)\n"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[{'publisher': 'ELSEVIER', 'doi': '10.1016/j.nucmedbio.2013.05.012', 'title': '(R)-[11C]verapamil is selectively transported by murine and human P-glycoprotein at the blood\\xd0brain barrier, and not by MRP1 and BCRP.', 'journal': 'Nuclear Medicine and Biology', 'source': 'fwf-13', 'cost': ' \\xdb 2,676.26 ', 'manual_status': 'OA', 'type': 'Hybrid Open Access'}, {'publisher': 'ELSEVIER', 'doi': '10.1016/j.biombioe.2012.11.022', 'title': '\\xd4Energy landscapes\\xd5: Meeting energy demands and human aspirations.', 'journal': 'Biomass and Bioenergy', 'source': 'fwf-13', 'cost': ' \\xdb 2,980.06 ', 'manual_status': 'OA', 'type': 'Hybrid Open Access'}]\n"
       ]
      }
     ],
     "prompt_number": 59
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Initial Processing and Cleanup\n",
      "------------------------------"
     ]
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###Cleaning up DOIs###\n",
      "\n",
      "We need to do some basic cleanup and normalisation here as well as probably some deduplication at some point. Firstly how many articles do we have and how many of those have DOIs."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "print len(articles), 'articles in total'\n",
      "print len([a for a in articles if a.get('doi') == None or a.get('doi')[0:3] != '10.']), 'rows without DOIs'\n",
      "print [a.get('doi') for a in articles if (a.get('doi') is not None and a.get('doi')[0:3] != '10.')]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "6530 articles in total\n",
        "3117 rows without DOIs\n",
        "['0.1016/j.tins.2013.08.001', '0.1093/ije/dyt086', '0.1111/cch.12031', 'none', 'none', 'none', 'none', 'none', 'none', 'none', 'none', 'none', 'none', 'none', 'none', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', '', ' 10.1037/a0034492', ' 10.1098/_rsif.2014.0034 ', '23733285', '', '24149150', '', '23458731', '']\n"
       ]
      }
     ],
     "prompt_number": 60
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "There is a problem with the first three DOIs from the Wellcome set that are clearly missing a '1' from the front of the DOI. There are also two DOIs with leading spaces along and a lot of mucky entries of empty strings and the string 'none. We need to do a quick cleanup. The FWF dataset has three PMIDs but these articles do not have DOIs so we will leave them as they are."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for a in articles:\n",
      "    doi = a.get('doi', 'NoneString')\n",
      "    if doi.startswith('0.1'):\n",
      "        a['doi'] = '1' + a.get('doi')\n",
      "        \n",
      "    elif doi == []:\n",
      "        print 'found-it'\n",
      "        a['doi'] = None\n",
      "        \n",
      "    elif doi.startswith(' 10.1'):\n",
      "        a['doi'] = a.get('doi').lstrip()\n",
      "    \n",
      "    elif doi == 'none':\n",
      "        a['doi'] = None\n",
      "\n",
      "    elif doi == '':\n",
      "        a['doi'] = None\n",
      "        \n",
      "    elif doi.isdigit():\n",
      "        a['doi'] = doi  \n",
      "        \n",
      "[a for a in articles if (a.get('doi') is not None and a.get('doi')[0:3] != '10.')]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 61,
       "text": [
        "[{'cost': ' \\xdb 500.00 ',\n",
        "  'doi': '23733285',\n",
        "  'journal': 'Geospatial health',\n",
        "  'manual_status': 'pure',\n",
        "  'publisher': 'International Society of Geospatial Health - GnosisGIS',\n",
        "  'source': 'fwf-13',\n",
        "  'title': 'Does altitude moderate the impact of lithium on suicide? A spatial analysis of Austria.'},\n",
        " {'cost': ' \\xdb 440.00 ',\n",
        "  'doi': '24149150',\n",
        "  'journal': 'Journal of Sports Science and Medicine',\n",
        "  'manual_status': 'pure',\n",
        "  'publisher': 'UNIVERSITY OF ULUDAG',\n",
        "  'source': 'fwf-13',\n",
        "  'title': 'Landing techniques in Beach Volleyball '},\n",
        " {'cost': ' \\xdb 1,653.50 ',\n",
        "  'doi': '23458731',\n",
        "  'journal': 'Oncotarget',\n",
        "  'manual_status': 'hybrid',\n",
        "  'publisher': 'IMPACT JOURNALS LLC',\n",
        "  'source': 'fwf-13',\n",
        "  'title': 'STAT5 triggers BCR-ABL1 mutation by mediating ROS production in chronic myeloid leukaemia.'}]"
       ]
      }
     ],
     "prompt_number": 61
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###Cleaning up costs###\n",
      "\n",
      "We have a mixture of pounds and euros in the dataset as well as some poor formatting resulting from data coming through multiple sources. Here we will define a quick cleanup mechanism and split the cost field into two, one for the amount one for the units. We can always split out the FWF data later."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def costcleanup(string):\n",
      "    if string and string.startswith(' \\xdb'):\n",
      "        value = ''.join(string[3:len(string)+1].split(','))\n",
      "        return 'EUR', float(value)\n",
      "    \n",
      "    elif string and string.startswith('\\xa3'):\n",
      "        value = ''.join(string[1:len(string)+1].split(','))\n",
      "        return 'GBP', float(value)\n",
      "    \n",
      "    elif string == None:\n",
      "        return None, None\n",
      "    \n",
      "    else:\n",
      "        return None, None\n",
      "    \n",
      "for a in articles:\n",
      "    currency, cost = costcleanup(a.get('cost', 'NoneString'))\n",
      "    if currency:\n",
      "        a['currency'] = currency\n",
      "        a['cost'] = cost\n",
      "\n",
      "print [a.get('cost') for a in articles if a.get('currency') != 'GBP' and a.get('currency') != 'EUR'] "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "[]\n"
       ]
      }
     ],
     "prompt_number": 62
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "###Collecting more dois for analysis###\n",
      "\n",
      "Most of our analysis will depend on having a DOI so for those entries where we don't have a DOI we need to try and get one. The Wellcome Trust data from 2010-12 is the main contributor to this set with some others coming from the Wellcome Trust 2012-13 dataset."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "dois = [article.get('doi') for article in articles]\n",
      "tofix = [index for index in range(len(dois)) if dois[index] == None]\n",
      "print len(tofix), 'articles without DOIs'\n",
      "for i in tofix[0:3001:500]:\n",
      "    print articles[i]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "3109 articles without DOIs\n",
        "{'publisher': 'JSciMed Central', 'doi': None, 'title': \"Parkinson's Disease: The Catabolic Theory\", 'journal': 'Journal of Neurology & Translational Neuroscience', 'currency': 'GBP', 'source': 'wellcome-12-13', 'cost': 159.91, 'manual_license': 'Publisher copyright', 'manual_status': None}\n",
        "{'publisher': 'Elsevier', 'source': 'wellcome-10-11', 'journal': 'Developmental Biology', 'title': 'Wake-up-call, a lin-52 paralogue, and Always early, a lin-9 homologue physically interact, but have opposing functions in gulatng testis-specific gene expression', 'currency': 'GBP', 'cost': 2379.72}\n",
        "{'publisher': 'Oxford University Press', 'source': 'wellcome-10-11', 'journal': 'Nucleic Acids Research', 'title': 'Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation.', 'currency': 'GBP', 'cost': 834.25}\n",
        "{'publisher': 'American Chemical Society', 'source': 'wellcome-11-12', 'journal': 'Journal of Proteome Research', 'title': 'Proteomic plasma membrane profiling reveals an essential role for gp96 in the cell surface expression of LDLR family members, including the LDL receptor and LRP6', 'currency': 'GBP', 'cost': 1314.0}\n",
        "{'publisher': 'Elsevier', 'source': 'wellcome-11-12', 'journal': 'Journal of Molecular Biology', 'title': 'Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis.', 'currency': 'GBP', 'cost': 2127.79}\n",
        "{'publisher': 'Public Library of Science', 'source': 'wellcome-11-12', 'journal': 'PLOS Neglected Tropical Diseases', 'title': \"Anopheles gambiae Antiviral Immune Response to Systemic O'nyong-nyong Infection\", 'currency': 'GBP', 'cost': 1662.66}\n",
        "{'publisher': 'Wiley-Blackwell', 'source': 'wellcome-11-12', 'journal': 'Hepatology', 'title': 'Estimating the Net Contribution of Interleaking-28B Variation to Spotaneous Hepatitis C Virus Clearence', 'currency': 'GBP', 'cost': 2580.97}\n"
       ]
      }
     ],
     "prompt_number": 63
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "We will use the Crossref API to get DOIs for those articles where we don't have them. The Crossref API is pretty good at identifying an article from its title and journal so we send those and get a response back. We also need to clean up those articles with non-standard characters and line breaks in them."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def is_ascii(s):\n",
      "    try:\n",
      "        s.decode('ascii')\n",
      "        return True\n",
      "    except UnicodeDecodeError:\n",
      "        return False\n",
      "\n",
      "for article in articles:\n",
      "    title = article.get('title')\n",
      "    if not is_ascii(title):\n",
      "        replace = []\n",
      "        for i, char in enumerate(title):\n",
      "            if not is_ascii(char):\n",
      "                replace.append((i, char))\n",
      "        replace.reverse()\n",
      "        for i, char in replace:\n",
      "            title = title[0:i] + title[i+1:len(title)+1]\n",
      "\n",
      "        article['title'] = title\n",
      "        print article.get('title')"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Defective TNF release from Crohns disease macrophages in response to Toll-like receptor activation: relationship to phenotype and genome-wide association susceptibility loci\n",
        "Normalizing the supernormal: The formation of the Gesellschaft fr Psychologische Forschung (Society for Psychological Research), c. 1886-1890\n",
        "Dissecting the mechanisms responsible for the multiple insecticide resistance phenotype in Anopheles gambiae s.s., M form, from Valle de Kou, Burkina Faso\n",
        "Is the environmental setting associated with the intensity and duration of childrens physical activity? Findings from the SPEEDY GPS study\n",
        "Food and social complexity at ayn Tepesi, southeastern Anatolia: Stable isotope evidence of differentiation in diet according to burial practice and sex in the early Neolithic\n",
        "The making of urban healtheries: Lord Brabazon and the transformation of cemeteries and burial grounds in late-Victorian East London\n",
        "A mechanistic explanation of the multiple helical forms adopted by bacterial flagellar filaments\n",
        "Examining multiple parenting behaviours on young childrens dietary fat consumption\n",
        "Effect of a serogroup A meningococcal conjugate vaccine (PsATT) on serogroup A meningococcal meningitis and carriage in Chad: a community study\n",
        "5-HTTLPR  environment interplay and its effects on neural reactivity in adolescents\n",
        "Deletion of Crry, the murine ortholog of the sporadic Alzheimers disease risk gene CR1, impacts tau phosphorylation and brain CFH\n",
        "Parent awareness of young childrens physical activity\n",
        "Making space for criminalistics: Hans Gross and fin-de-sicle CSI\n",
        "Patients beliefs about the causes, persistence and control of psychotic experiences predict take-up of effective cognitive behaviour therapy for psychosis\n",
        "Tracking sickness through social networks  the practical use of social network mapping in supporting the management of an E.coli O157 outbreak in a primary school in London\n",
        "Amyloid-_ and Alzheimers disease type pathology differentially affects the calcium signalling toolkit in astrocytes from different brain regions\n",
        "Prdm14 promotes germline fate and nave pluripotency by7 repressing FGF signalling and DNA methylation\n",
        "A role for piezo2 in EPAC1 dependent mechanical allodynia\n",
        "Astrocytes and glutamate homeostasis in Alzheimers disease: a decrease in glutamine synthetase but not in glutamate transporter-1 in the prefrontal cortex.\n",
        "Cell Cycle-dependent Regulation of the Forkhead Transcription Factor FOXK2 by CDKCyclin Complexes\n",
        "Estrogen receptor  mediates proliferation of osteoblastic cells stimulated by estrogen and mechanical strain, but their acute down regulation of the Wnt antagonist Sost is mediated by Estrogen Receptor \n",
        "Prenatal exposures and anti-Mllerian hormone in female adolescents: the Avon Longitudinal Study of Parents and Children\n",
        "The role of interleukin10 family of cytokines in HIVtuberculosis associated immune reconstitution inflammatory syndrome\n",
        "Refuse and the Risk Society: The Political Ecology of Risk in Inter-war Britain\n",
        "Endothelial cell junctional adhesion molecule plays a key role in the development of tumours in a murine model\n",
        "Telamere length measurement can distinguish pathogenic from non-pathogenic var\n",
        "The long-term safety and efficacy of bilateral transplantation of human fetal striatal tissue in patients with mild to moderate Huntingdons disease\n",
        "The pursuit of happiness: the social and scientific origins of Hans Selyes natural philosophy of life\n",
        "Upper Airways Microbiota in Antibiotic-Nave Wheezing and Healthy Infants from the Tropics of Rural Ecuador\n",
        "Vitamin B-12 status during pregnancy and childs IQ at age 8: A Mendelian randomization study in the Avon Longitudinal Study of Parents and Children\n",
        "A Molecular Phylogeny of Plesiorycteropus Reassigns the Extinct Mammalian Order Bibymalagasia\n",
        "Anti-Mllerian hormone is not associated with cardiometabolic risk factors in adolescent females\n",
        "An activating mutation reveals a second binding mode of the integrin 2 I domain to the GFOGER motif in collagens\n",
        "What is value  accumulated reward or evidence?\n",
        "Quantitative multiparameter mapping of R1, PD*, MT and R2* at 3T: a multicenter validation\n",
        "Mothers own recollections of being parented and risk of offsprings depression 18 years later: A prospective cohort study\n",
        "Molecular  detection of mixed infections of Mycobacterium tuberculosis \n",
        "Eicosapentaenoic acid and docosahexaenoic acid reduce interleukin-1-mediated cartilage degradation.\n",
        "Glycoproteomic characterization of carriers of the CD15/Lewisx epitope on Hodgkins Reed-Sternberg cells\n",
        "Neurologists understanding and management of conversion disorder\n",
        "Microtubule stabilization in vivo by nucleation-incompetent _-tubulin complex.\n",
        "Carers Attributions about Positive Events in Psychosis Relate to Expressed Emotion.  Behaviour Research and Therapy. 47:783-789\n",
        "Horizontal biases in rats use of three-dimensional space\n",
        "Identification and characterisation of the BPI/LBP/PLUNClike gene repertoire in chickens reveals the absence of a LBP gene\n",
        "A good hospital: Nurse and patient perceptions of good clinical care for HIV positive people on antiretroviral treatment in rural Zimbabwe\n",
        "Hunting with a knife and fork': Examining Central Coherence in autism, ADHD and typical development with a linguistic task\n",
        "Presence and Severity of Non-alcoholic Fatty Liver Disease in a Large Prospective Primary Care Cohort\n",
        "Myocardial stress remodelling after regional infarction is independent of glycogen synthase kinase-3 inactivation\n",
        "Behaviour problems and prevalence of asthma symptoms among Brazilian children'\n",
        "Investigating environmental  links between maternal depression symptoms and child anxiety/depression symptoms using a genetic design; the effects of shared adversity..\n",
        "Effect of single-dose anthelmintic treatment during pregnancy \n",
        "Predicting clinical scores from magnetic resonance scans in Alzheimers disease\n",
        "Model-based influences on humans choices and striatal prediction errors\n",
        "Evolution of beta blockers  from anti-angina drugs to ligand directed signalling\n",
        "Effects of maternal and infant co-infections, and maternal immunisation \n",
        "Health Status of Adults with Congenital Adrenal Hyperplasia:A Cohort Study of 203 Patients\n",
        "\n",
        "Systemic effector and regulatory immune responses to chlamydial antigens \n",
        "Expression of the neuronal adaptor protein X11alpha protects against memory dysfunction in a transgenic mouse model of Alzheimers disease\n",
        "Nuclear actin and transcriptional activation.  Published as an addendum to Nuclear actin polymerization is required\n",
        "for transcriptional reprogramming of Oct4\n",
        "by oocytes. Genes Dev 2011; 25:94658;\n",
        "PMID: 21536734\n",
        "Maternity Charities, the Edinburgh Maternity Scheme and the Medicalisation of Childbirth, 19001925\n",
        "The pharmocological effects of the thermostabilising (m23) mutations & intra & extracellular (36) deletions essential for crytallisation of the turkey -adrenoceptor\n",
        "NATRIURETIC PEPTIDE RECEPTORC UNDERPINS THE DISPARATE REGULATION OF ENDOTHELIAL AND VASCULAR SMOOTH MUSCLE CELL PROLIFERATION BY C-TYPE NATRIURETIC PEPTIDE\n",
        "Can AIDS stigma be reduced to poverty stigma? Exploring Zimbabwean childrens representations of poverty and AIDS\n",
        "What should be done when thyroid function tests dont make sense\n",
        "Concurrent TMSfMRI reveals dynamic interhemispheric influences of the right parietal cortex during exogenously cued visuospatial attention\n",
        "A type III effector protease NleC from enteropathogenic Escherichia coli targets NF-B for degradation \n",
        "Childrens antisocial behavior, mental health, drug use, and educational performance after parental incarceration: A systematic review and meta-analysis\n",
        "Patients rights and the national health service in britain, 1960s-1980s.\n",
        "Impaired self  other differentiation in frontotemporal dementia\n",
        "Effects of maternal worm infections and anthelminthic treatment during pregnancy on infant .\n",
        "Automated carotid IMT measurement and its validation in low contrast ultrasound database of 885 patient Indian population epidemiological study: results of AtheroEdge Software\n",
        "New CD1d Agonists:  Synthesis and Biological Activity of 6-Triazole-Substituted <alpha>-Galactosyl Ceramides\n",
        "A torque-based method demonstrates increased rigidity in Parkinsons disease during low-frequency stimulation\n",
        "The generation and evaluation of two panels of epitope-matched mouse IgG1, IgG2a, IgG2b and IgG3 antibodies specific for Plasmodium falciparum and Plasmodium yoelii merozoite surface protein 119 (MSP119) Original Research Articl\n",
        "Interventional studies for preventing Surgical Site Infections in sub-Saharan Africa  a systematic review\n",
        "\n",
        "A nexus for gene expression  molecular mechanisms of Spt5 and NusG in the three domains of life\n",
        "Dynamic causal modelling of precision and synaptic gain in visual perception  an EEG study\n",
        "Lateralised visual attention is unrelated to language lateralisation, and not influenced by task difficulty  A functional transcranial Doppler study\n",
        "Scant evidence for Spearmans Law of diminishing returns in middle childhood. (2007)\n",
        "Tibetan wind and wind illnesses: towards a multicultural approach to health and illness\n",
        "Clonal Growth of Dermal Papilla Cells in Hydrogels reveals intrincis differences between Sox2-positive and negative cells in vitro and in vivo\n",
        "JAK/STAT3 signalling is sufficient and dominant over antagonistic cues for the establishment of nave pluripotency\n",
        "Dopamine and performance in a reinforcement learning task  evidence from Parkinsons disease\n",
        "False recognition in a mouse model of Alzheimers disease: rescue with sensory restriction and memantine \n",
        "The cardiac sodium channel mutation delQKP 15071509 is associated with the expanding phenotypic spectrum of LQT3, conduction disorder, dilated cardiomyopathy, and high incidence of youth sudden death\n",
        "Genetic variation in the 15q25 nicotinic acetylcholine receptor gene cluster (CHRNA5CHRNA3CHRNB4) interacts with maternal self-reported smoking status during pregnancy to influence birth weight\n",
        "Trends and inequalities in cardiovascular disease mortality across 7932 English wards, 19822006: Bayesian spatial analysis\n",
        "A Human Challenge Model for Mycobacterium tuberculosis Using Mycobacterium bovis Bacille Calmette-Gurin\n",
        "\n",
        "Dissociation from DNA of Type III RestrictionModification enzymes during helicase-dependent motion and following endonuclease activity\n",
        "Specialisation of an Exonuclease III family enzyme in the repair of 3 DNA lesions during base excision repair in the human pathogen Neisseria meningitidis\n",
        "Priming for self-esteem influences the monitoring of ones own performance\n",
        "The Orthologue of Sjgren's Syndrome Nuclear Autoantigen 1 (SSNA1) in Trypanosoma brucei is an Immunogenic Self-Assembling Molecule.\n",
        "Factors That Promote H3 Chromatin Integrity during Transcription Prevent Promiscuous Deposition of CENP-ACnp1in Fission Yeast\n",
        "Correlation of inter-locus polyglutamine toxicity with CAGCTG triplet repeat expandability and flanking genomic DNA GC content\n",
        "Experimental evolution of a bacteriophage virus reveals the trajectory adaption across a fecund\n",
        "Psychical research and the origins of American psychology: Hugo Mnsterberg, William James and Eusapia Palladino\n",
        "Orbital fibrosis in a mouse model of Graves disease induced by genetic immunization of  thyrotropin receptor cDNA\n",
        "Molecular mechanisms of muscarinic acetylcholine receptorstimulated increase in cytosolic free Ca2+ concentration and ERK1/2 activation in the MIN6 pancreatic _-cell line\n",
        "\n",
        "Improving Questions on Sexual Partnerships: Lessons Learned from Cognitive Interviews for Britains Third National Survey of Sexual Attitudes and Lifestyles (Natsal-3)\n",
        "Read-Right: a web app that improves reading speeds in patients with hemianopia\n",
        "B-Cell Repopulation After Alemtuzumab InductionTransient Increase in Transitional B cells and Long-Term Dominance of Nave B Cells\n",
        "A briefdementia screener suitable for use by non-specialists in resource poor settings--the cross-cultural derivation and validation of the brief Community Screening Instrument for Dementia\n",
        "Satellite Lesions in Congenital Melanocytic NeviTime for a Change of Name\n",
        "Computational Analysis Predicts the Kaposis Sarcoma-Associated Herpesvirus Tegument Protein ORF63 to be Alpha Helical\n",
        "Molecular mechanism and physiological role of activedeactive transition of mitochondrial complex I\n",
        "Sugar-derived organogels as templates for structured, photoluminescent conjugated polymerinorganic hybrid materials\n",
        "A method and tool for cradle to grave embodied carbon and energy impacts of UK buildings\n",
        "The Rumsfeld paradox: Some of the things we know that we dont know about plant virus infection\n",
        "Creating obesogenic realities; do our methodological choices make a difference when measuring the food environment?\n",
        "Childrens sedentary behaviour: Descriptive epidemiology and associations with objectively-measured sedentary time.\n",
        "How do couples influence each others physical activity behaviours in retirement? An exploratory qualitative study\n",
        "Functionally different pads on the same foot allow control of attachment: stick insects have load-sensitive heel pads for friction and shear-sensitive toe pads for adhesion\n",
        "Surface contact and design of fibrillar friction pads in stick insects (Carausius morosus): mechanisms for large friction coefficients and negligible adhesion\n",
        "(R)-[11C]verapamil is selectively transported by murine and human P-glycoprotein at the bloodbrain barrier, and not by MRP1 and BCRP.\n",
        "Energy landscapes: Meeting energy demands and human aspirations.\n",
        "I dont think I could, you know, just teach without any emotion: exploring the nature and origin of university teachers emotions.\n",
        "Just War and Holy War in the Middle Ages.\n",
        "Green electronics: biodegradable and biocompatible materials and devices for sustainable future.\n",
        "I dont hide my feelings, even though I try to: insight into teacher educator emotion display.\n",
        "Translating between survey answer formats.\n",
        "Siehe, Magier kamen aus dem Osten: Eine Paraphrase der Magier-Perikope aus dem Matthusevangelium (Mt 2,1-12).\n",
        "2-Supernilpotent Malcev algebras.\n",
        "A Modified Synthetic Pathway for the Synthesis of so far Inaccessible N1-Functionalized Tetrazole Ligands  Synthesis and Characterization of the 1D Chain-Type Spin Crossover Compound [Fe(3ditz)3](BF4)2.\n",
        "A new radiocarbon chronology of Baumkirchen, stratotype for the onset of the Upper Wrmian in the Alps.\n",
        "Alloying-related trends from first principles: An application to the TiAlXN system.\n",
        "Alpha/beta-Hydrolase Domain Containing Protein 15 (ABHD15)  an Adipogenic Protein Protecting from Apoptosis.\n",
        "An SCC-DFTB Repulsive Potential for Various ZnO Polymorphs and the ZnOWater System.\n",
        "Assessing the impact of transitions from centralised to decentralised water solutions on existing infrastructures  Integrated city-scale analysis with VIBe.\n",
        "Asymmetric bioreduction of activated carboncarbon double bonds using Shewanella yellow enzyme (SYE-4) as novel enoate reductase.\n",
        "Byzantinische Nekropole und normannenzeitlicher Kirchenbau. Eine Auswertung von Fundkomplexen sptantiker bis frhneuzeitlicher Zeitstellung anhand des keramischen Materials.\n",
        "Cage-Forming Compounds in the BaRhGe System: From Thermoelectrics to Superconductivity.\n",
        "Calorimetric studies of CuLi, LiSn, and CuLiSn.\n",
        "Calorimetric study of the entropy relation in the NaClKCl system.\n",
        "Characterization of the Fe-rich corner of AlFeSiTi.\n",
        "Chiral Hydroxylation at the Mononuclear Nonheme Fe(II) Center of 4-(S) Hydroxymandelate Synthase  A Structure-Activity Relationship Analysis.\n",
        "Combating the epigenome: epigenetic drugs against non-Hodgkins lymphoma.\n",
        "Comparison between MICROCARDFISH and 16S rRNA gene clone libraries to assess the active versus total bacterial community in the coastal Arctic.\n",
        "Complex Polymorphic System of Gallic AcidFive Monohydrates, Three Anhydrates, and over 20 Solvates.\n",
        "Conservation of Protists: The Krauthgel Pond in Austria.\n",
        "Der Multiradikalcharakter ein- und zweidimensionaler Graphen-Nanobnder\n",
        "Die Perikope von der Hochzeit zu Kana ( Joh 2:1-11) im Kontext der Sptantike . 2013.\n",
        "Dielectric Function of Undoped and Doped Poly[2-methoxy-5-(3,7-dimethyloctyloxy)-1,4-phenylene-vinylene] by Ellipsometry in a Wide Spectral Range.\n",
        "Dont get the blues: conspicuous nuptial colouration of male moor frogs (Rana arvalis) supports visual mate recognition during scramble competition in large breeding aggregations.\n",
        "Effect of MoleculeSurface Reaction Mechanism on the Electronic Characteristics and Photovoltaic Performance of Molecularly Modified Si.\n",
        "Epigenomics of cancer  emerging new concepts.\n",
        "Ethnopharmacological in vitro studies on Austria's folk medicineAn unexplored lore in vitro anti-inflammatory activities of 71 Austrian traditional herbal drugs.\n",
        "Experimental partitioning of halogens and other trace elements between olivine, pyroxenes, amphibole and aqueous fluid at 2 GPa and 9001,300 GradC.\n",
        "Explaining coalition bargaining outcomes: Evidence from Austria, 20022008.\n",
        "Explaining the Temperature Dependence of Spirilloxanthins S* Signal by an Inhomogeneous Ground State Model.\n",
        "Explorative Learning and Functional Inferences on a Five-Step Means-Means-End Problem in Goffins Cockatoos (Cacatua goffini).\n",
        "Factors That Limit Positron Emission Tomography Imaging of P-Glycoprotein Density at the BloodBrain Barrier.\n",
        "Fearless Dominance and reduced feedback-related negativity amplitudes in a time-estimation task  Further neuroscientific evidence for dual-process models of psychopathy.\n",
        "FGF23 acts directly on renal proximal tubules to induce phosphaturia through activation of the ERK1/2SGK1 signaling pathway.\n",
        "First selective direct mono-arylation of piperidines using ruthenium-catalyzed CH activation.\n",
        "Flatness of Semilinear Parabolic PDEsA Generalized CauchyKowalevski Approach.\n",
        "Global socioeconomic carbon stocks in long-lived products 19002008 .\n",
        "Hamiltonian mass of asymptotically Schwarzschildde Sitter space-times.\n",
        "Heterolytic Cleavage of Dihydrogen by an Iron(II) PNP Pincer Complex via MetalLigand Cooperation.\n",
        "Histone H3 phosphorylation  A versatile chromatin modification for different occasions.\n",
        "How endangered is sexual reproduction of high-mountain plants by summer frosts?  Frost resistance, frequency of frost events and risk assessment.\n",
        "How Far Could We Go with Open Data  A Case Study for TRPV1 Antagonists.\n",
        "Hydrogen-bonds in molecular solids  from biological systems to organic electronics.\n",
        "Inhibition of hepatic scavenger receptor-class B type I by RNA interference decreases atherosclerosis in rabbits.\n",
        "Inhibitory Function of the Dorsomedial Hypothalamic Nucleus on the HypothalamicPituitaryAdrenal Axis Response to an Emotional Stressor but not Immune Challenge.\n",
        "Integrated MachZehnder interferometer for BoseEinstein condensates.\n",
        "Interfacial Bond-Breaking Electron Transfer in Mixed WaterEthylene Glycol Solutions: Reorganization Energy and Interplay between Different Solvent Modes.\n",
        "Investigation of prescribed movement in fluidstructure interaction simulation for the human phonation process.\n",
        "Jatrophane Diterpenes  Preparation of the Western Fragment of Pl-3. European Journal of Organic Chemistry\n",
        "Level-k reasoning and time pressure in the 1120 money request game.\n",
        "Lipid Droplets and Peroxisomes: Key Players in Cellular Lipid Homeostasis or A Matter of FatStore em Up or Burn em Down.\n",
        "Manipulating MnMgk cation complexes to control the charge- and spin-state of Mn in GaN.\n",
        "Matrix Isolation Studies of Carbonic AcidThe Vapor Phase above the -Polymorph.\n",
        "Mechanism Elucidation of the cistrans Isomerization of an Azole RutheniumNitrosyl Complex and Its Osmium Counterpart.\n",
        "Mechanism of the Phospha-WittigHorner Reaction.\n",
        "Medical knowledge and the improvement of vernacular languages in the Habsburg Monarchy: A case study from Transylvania (17701830).\n",
        "Metabolic fingerprinting of Leontopodium species (Asteraceae) by means of 1H NMR and HPLCESI-MS\n",
        "MetalArene Complexes with Indolo[3,2-c]-quinolines: Effects of Ruthenium vs Osmium and Modifications of the Lactam Unit on Intermolecular Interactions, Anticancer Activity, Cell Cycle, and Cellular Accumulation.\n",
        "Methods for quantification of porevoltage sensor interaction in CaV1.2.\n",
        "Microbial processes and community composition in the rhizosphere of European beech  The influence of plant C exudates.\n",
        "Modeling diffusion-governed solidification of ternary alloys  Part 1: Coupling solidification kinetics with thermodynamics.\n",
        "Mutations in the -Tubulin Gene TUBB5 Cause Microcephaly with Structural Brain Abnormalities.\n",
        "Nationalization campaigns and teachers' practices in BelgianGerman and PolishGerman border regions (19451956).\n",
        "Neuropeptide Y and peptide YY protect from weight loss caused by Bacille CalmetteGurin in mice.\n",
        "Normal Mode Analysis of the Spectral Density of the FennaMatthewsOlson Light-Harvesting Protein: How the Protein Dissipates the Excess Energy of Excitons.\n",
        "Novel SolGel Precursors for Thin Mesoporous Eu3+-Doped Silica Coatings as Efficient Luminescent Materials.\n",
        "On conjugate families and Jeffreys priors for von MisesFisher distributions.\n",
        "On the Configurational Stability of Chiral Heteroatom-Substituted [D1]Methylpalladium Complexes as Intermediates of Stille and SuzukiMiyaura Cross-Coupling Reactions.\n",
        "Ostracods (Crustacea) and their palaeoenvironmental implication for the Solimes Formation (Late Miocene; Western Amazonia/Brazil).\n",
        "Oxaphospholes and Bisphospholes from Phosphinophosphonates and a,  Unsaturated Ketones.\n",
        "ztopcu , Kirchner K, et al: Reactivity of iron complexes containing monodentate aminophosphine ligands  Formation of four-membered carboxamido-phospha-metallacycles.\n",
        "Particle Networks from Powder Mixtures: Generation of TiO2SnO2 Heterojunctions via Surface Charge-Induced Heteroaggregation.\n",
        "Phase equilibria and structural investigations in the Ni-poor part of the system AlGeNi.\n",
        "Phase equilibria in the ternary In-Ni-Sn system at 700 C.\n",
        "Photochemical degradation study of polyvinyl acetate paints used in artworks by PyGC/MS.\n",
        "Physical scales in the WignerBoltzmann equation.\n",
        "Polyacetylenes from Notopterygium incisumNew Selective Partial Agonists of Peroxisome Proliferator-Activated Receptor-Gamma.\n",
        "Polyhalite microfabrics in an Alpine evaporite mlange: Hallstatt, Eastern Alps.\n",
        "Promoting interdisciplinary education  the Vienna Doctoral Programme on Water Resource Systems.\n",
        "Propeamussiidae, Inoceramidae, and other Bivalvia from the Lower Cretaceous Puez Formation (ValanginianCenomanian; Dolomites, South Tyrol, Italy).\n",
        "Prospects and limits of the flow cytometric seed screen  insights from Potentilla sensu lato (Potentilleae, Rosaceae)\n",
        "Protein Kinase C--Dependent Activation of NF-kB in Stromal Cells Is Indispensable for the Survival of Chronic Lymphocytic Leukemia B Cells In Vivo.\n",
        "Quantifying Thiol Ligand Density of Self-Assembled Monolayers on Gold Nanoparticles by Inductively Coupled PlasmaMass Spectrometry.\n",
        "Sensitivity of Aspergillus nidulans to the Cellulose Synthase Inhibitor Dichlobenil: Insights from Wall-Related Genes Expression and Ultrastructural Hyphal Morphologies.\n",
        "Shielding effects in polymerpolymer reactions. V. Concentration dependence of contact formation between star-branched and linear chains. Polymer, Volume 54, Issue 16, 19 July 2013, Pages 41834193\n",
        "doi: 10.1016/j.polymer.2013.05.055\n",
        "SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LCMS Performance Metrics on Orbitrap Instruments.\n",
        "Single-channel properties of a34, a34a5 and a342 nicotinic acetylcholine receptors in mice lacking specific nicotinic acetylcholine receptor subunits.\n",
        "Soil metaproteomics  Comparative evaluation of protein extraction protocols.\n",
        "Sphingosine 1-Phosphate Counteracts the Effects of Interleukin-1 in Human Chondrocytes.\n",
        "Stable optical oxygen sensing materials based on click-coupling of fluorinated platinum(II) and palladium(II) porphyrinsA convenient way to eliminate dye migration and leaching.\n",
        "StructuralFunctional Studies of Burkholderia cenocepaciad-Glycero-d-manno-heptose 7-Phosphate Kinase (HldA) and Characterization of Inhibitors with Antibiotic Adjuvant and Antivirulence Properties.\n",
        "Studies of atomic diffusion in NiPt solid solution by x-ray photon correlation spectroscopy.\n",
        "Synthesis and Properties of Highly Dispersed Ionic SilicaPoly(ethylene oxide) Nanohybrids.\n",
        "Systems biology of hostfungus interactions: turning complexity into simplicity\n",
        "Tensile Lattice Strain Accelerates Oxygen Surface Exchange and Diffusion in La1xSrxCoO3 Thin Films.\n",
        "The 2.5  Structure of the Enterococcus Conjugation Protein TraM resembles VirB8 Type IV Secretion Proteins.\n",
        "The degree profile of random Plya trees.\n",
        "The EORTC emotional functioning computerized adaptive test: phases IIII of a cross-cultural item bank development.\n",
        "The grain and grain boundary impedance of solgel prepared thin layers of yttria stabilized zirconia (YSZ).\n",
        "The Haselgebirge evaporitic mlange in central Northern Calcareous Alps (Austria): Part of the Permian to Lower Triassic rift of the Meliata ocean?\n",
        "The impact of a financial transaction tax on stylized facts of price returnsEvidence from the lab.\n",
        "The Importance of the Secure Base Effect for Domestic Dogs  Evidence from a Manipulative Problem-Solving Task.\n",
        "The issue agenda, party competence and popularity: An empirical analysis of Austria 19892004.\n",
        "The power of AAA-ATPases on the road of pre-60S ribosome maturation  Molecular machines that strip pre-ribosomal particles.\n",
        "The role of interleukin 1 in human trophoblast motility.\n",
        "Theoretical Investigations and Density Functional Theory Based Quantitative StructureActivity Relationships Model for Novel Cytotoxic Platinum(IV) Complexes.\n",
        "ThueMorse at multiples of an integer\n",
        "Time optimal controls of the linear FitzhughNagumo equation with pointwise control constraints.\n",
        "Toddlers transition to out-of-home day care: Settling into a new care environment.\n",
        "Tropaeolum Tops Tobacco  Simple and Efficient Transgene Expression in the Order Brassicales.\n",
        "Understanding Structure and Bonding of Multilayered MetalOrganic Nanostructures.\n",
        "Vivid valleys, pallid peaks? Hypsometric variations and ruralurban land change in the Central Peruvian Andes.\n",
        "What Reasons Might the Other One Have?Perspective Taking to Reduce Psychological Reactance in Individualists and Collectivists.\n"
       ]
      }
     ],
     "prompt_number": 64
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Still a few problems with bad characters in journal names. These are easiest to fix manually at this stage. Crossref is giving some strange internal server error for the NAR paper on FokI restriction endonuclease."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "articles[2373]['journal'] = 'Annals of the Rheumatic Diseases'\n",
      "articles[3006]['title'] = 'Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer' \n",
      "articles[3319]['journal'] = 'Journal of Inherited Metabolic Diseases'"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 65
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def doifromcrossref(title, journal, index):\n",
      "    urlbase = 'http://search.crossref.org/dois?'\n",
      "    params = {'q' : ', '.join([title, journal])}\n",
      "    try:\n",
      "        resp = requests.get(urlbase, params=params)\n",
      "        resp.raise_for_status()\n",
      "        return resp.json()\n",
      "    \n",
      "    except requests.exceptions.HTTPError, e:\n",
      "        print 'HTTPError:', e\n",
      "        print title, journal, index\n",
      "\n",
      "responses = []\n",
      "for i in tofix:\n",
      "    responses.append(doifromcrossref(articles[i].get('title'), articles[i].get('journal'), i))"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "HTTPError: 500 Server Error: Internal Server Error\n",
        "Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer Nucleic Acids Research 3006\n"
       ]
      }
     ],
     "prompt_number": 66
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "def checkcrossref(indexes, responses):\n",
      "    fixed = []\n",
      "    notfixed = []\n",
      "\n",
      "    for i, resp in enumerate(responses):\n",
      "        if resp is not None and (resp[0].get('score')> 2):\n",
      "            fixed.append((indexes[i], resp[0]['doi'], resp[0]['title'], articles[indexes[i]].get('title')))\n",
      "        elif resp is not None:\n",
      "            notfixed.append((indexes[i], resp[0]['doi'], resp[0]['title'], articles[indexes[i]].get('title')))\n",
      "        \n",
      "    return fixed, notfixed"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 67
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "fixed, notfixed = checkcrossref(tofix, responses)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 68
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "len(fixed)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 69,
       "text": [
        "2943"
       ]
      }
     ],
     "prompt_number": 69
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for nf in notfixed:\n",
      "    print nf\n",
      "        "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "(2012, u'http://dx.doi.org/10.1017/cbo9780511980053.012', u\"Parkinson's disease\", \"Parkinson's Disease: The Catabolic Theory\")\n",
        "(2013, u'http://dx.doi.org/10.1111/maq.12030', u'Evidence, Ethos and Experiment: The Anthropology and History of Medical Research in Africa. P. WenzelGeissler and CatherineMolyneux, eds. New York: Berghahn Books 2011; 498 pp.', 'Parasite lost - remembering modern times with Kenyan government medical scientists.')\n",
        "(2014, u'http://dx.doi.org/10.1111/maq.12030', u'Evidence, Ethos and Experiment: The Anthropology and History of Medical Research in Africa. P. WenzelGeissler and CatherineMolyneux, eds. New York: Berghahn Books 2011; 498 pp.', 'Studying trial Communities: anthropological and historical enquiries and ethos, politics and economy of medical research in Africa.')\n",
        "(2016, u'http://dx.doi.org/10.1139/o80-025', u'pH-Dependent amino acid induced conformational changes of rabbit muscle pyruvate kinase', 'Pyruvate kinase is a dosage-dependent regulator of cellular amino acid homeostasis')\n",
        "(2017, u'http://dx.doi.org/10.1158/1078-0432.ccr-05-2105', u'Expression of DNA Double-Strand Break Repair Proteins ATM and BRCA1 Predicts Survival in Colorectal Cancer', 'Loss of expression of the double strand break repair protein ATM is associated with worse prognosis in colorectal cancer and loss of Ku70 expression is associated with CIN.')\n",
        "(2026, u'http://dx.doi.org/10.1093/hmg/ddt439', u'The familial dementia gene revisited: a missense mutation revealed by whole-exome sequencing identifies ITM2B as a candidate gene underlying a novel autosomal dominant retinal dystrophy in a large family', 'Whole exome sequencing identifies a novel variant in APOB causing accumulation of circulating mutant LDL in a family with autosomal dominant hypercholesterolaemia')\n",
        "(2027, u'http://dx.doi.org/10.1109/embc.2013.6610257', u'Automated IMT estimation and BMI correlation using a low-quality carotid ultrasound image database from India', 'Correlation of automated IMT and BMI in an image database from India on a very low resolution carotid ultrasound.')\n",
        "(2030, u'http://dx.doi.org/10.1196/annals.1367.017', u'Serotonin and Norepinephrine Reuptake Inhibition and Eating Behavior', 'How serotonin shapes moral judgment and behavior')\n",
        "(2043, u'http://dx.doi.org/10.1111/(issn)1600-065x', u'Immunological Reviews', 'Actin cytoskeletal defects in immunodeficiency')\n",
        "(2049, u'http://dx.doi.org/10.1111/j.1471-8731.2004.00065.x', u'Rethinking Medical Ethics: A View From Below', 'Rethinking biomedicine and governance in Africa:Contributions from anthropology')\n",
        "(2095, u'http://dx.doi.org/10.1111/bph.12287', u' A single channel mutation alters agonist efficacy at 5-HT 3 A and 5-HT 3 AB receptors ', 'A single channel mutation alters agonist efficacy at 5-HT3A and 5-HT3AB receptors')\n",
        "(2098, u'http://dx.doi.org/10.1113/jphysiol.2011.214759', u'Redefining the components of central CO2 chemosensitivity-towards a better understanding of mechanism', 'Redefining the component of cenral CO2 chemosensitivity')\n",
        "(2124, u'http://dx.doi.org/10.3791/4025', u'November 2011: This Month in JoVE', 'FILM - to be filmed in November')\n",
        "(2128, u'http://dx.doi.org/10.1016/s0033-3506(25)80183-5', u'Collected addresses and laboratory Studies\\u2014London School of Hygiene and Tropical Medicine', 'Laboratory Science in Tropical Medicine')\n",
        "(2139, u'http://dx.doi.org/10.1007/bfb0025286', u'Non-heme iron dioxygenases structure and mechanism', 'Structure and reaction mechanism in the heme dioxgenases')\n",
        "(2145, u'http://dx.doi.org/10.1016/j.bmcl.2003.11.059', u'Permeation and metabolism of a series of novel lipophilic ascorbic acid derivatives, 6-O-acyl-2-O-\\u03b1-d-glucopyranosyl-l-ascorbic acids with a branched-acyl chain, in a human living skin equivalent model', 'Novel Lipophilic Authohydroxamic acid derivatives...')\n",
        "(2148, u'http://dx.doi.org/10.1021/pr100446f', u'Proteomic Analysis of a Noninvasive Human Model of Acute Inflammation and Its Resolution: The Twenty-one Day Gingivitis Model', 'Proteomic analysi of a non invasive human model of acute contamination and its resolution : the 21st day gingintis model')\n",
        "(2149, u'http://dx.doi.org/10.1021/pr101021c', u' Novel Glycosylation Sites Localized in Campylobacter jejuni Flagellin FlaA by Liquid Chromatography Electron Capture Dissociation Tandem Mass Spectrometry ', 'Novel gylosylation sites localised in campylobalter jejuni flagellin flaa by lc eld mass spectonomy')\n",
        "(2158, u'http://dx.doi.org/10.1513/pats.200806-057qc', u'Quantitative Computed Tomography Assessment of Airway Wall Dimensions: Current Status and Potential Applications for Phenotyping Chronic Obstructive Pulmonary Disease', 'The role of computed tomography in multi-dimensional phenotyping of chronic obstructive pulomary disease')\n",
        "(2176, u'http://dx.doi.org/10.1074/jbc.m406212200', u'A Tissue-specific, Naturally Occurring Human SNF2L Variant Inactivates Chromatin Remodeling', '6154090 3644306 A naturally occurring variant in human TLR')\n",
        "(2177, u'http://dx.doi.org/10.1074/jbc.m110.159996', u'Two Human MYD88 Variants, S34Y and R98C, Interfere with MyD88-IRAK4-Myddosome Assembly', '6154715 3655631 Two human MYD88 variants, S34Y and R9')\n",
        "(2182, u'http://dx.doi.org/10.1074/jbc.m208339200', u'Mapping the Type I Collagen-binding Site on Pigment Epithelium-derived Factor. IMPLICATIONS FOR ITS ANTIANGIOGENIC ACTIVITY', 'IMPLICATIONS FOR COLLAGEN BINDING FROM THE CR')\n",
        "(2230, u'http://dx.doi.org/10.1074/jbc.m111.260364', u'Cysteine Scanning Mutagenesis (Residues Glu52-Gly96) of the Human P2X1 Receptor for ATP: MAPPING AGONIST BINDING AND CHANNEL GATING', 'Cystene Scanning mutogenesis  (residues EZ2 - 996) of the human P2X1 Receptor for ATP; Mapping against binding and channel gating')\n",
        "(2242, u'http://dx.doi.org/10.1111/j.1365-2958.2011.07952.x', u'BsrG/SR4 from Bacillus subtilis- the first temperature-dependent type I toxin-antitoxin system', 'The Structure and Interactions of SpollSA and SpollSB, a Toxin-Antitoxin System in Bacillus subtilis')\n",
        "(2244, u'http://dx.doi.org/10.1074/mcp.m111.009787', u'Unraveling Lactococcal Phage Baseplate Assembly by Mass Spectrometry', 'Unraveling lacococcal phages baseplate assembly by mass spectrometry')\n",
        "(2266, u'http://dx.doi.org/10.1093/ndt/gfm193', u'Complement hyperactivation may cause atypical haemolytic uraemic syndrome gain-of-function mutations in factor B', 'The development of atypical haemolytic uraemic syndrome in mice is dependent on complement C5')\n",
        "(2283, u'http://dx.doi.org/10.1167/iovs.09-5054', u'Pathway-Focused Arrays Reveal Increased Matrix Metalloproteinase-7 (Matrilysin) Transcription in Trachomatous Trichiasis', 'Conjunctival gene expression profiling using pathway focused arrays reveals increased\\nmatrix metalloproteinase-7 (matrilysin) transcription in trachomatous trichiasis')\n",
        "(2304, u'http://dx.doi.org/10.1186/1471-2202-12-91', u'A comparison of in vitro properties of resting SOD1 transgenic microglia reveals evidence of reduced neuroprotective function', '\\nA comparison of in vitro properties of resting\\nSOD1 tran\\nsgenic microglia reveals evidence of reduced neuroprotec\\n')\n",
        "(2367, u'http://dx.doi.org/10.1186/1745-6215-12-250', u\"A comparison of specialist rehabilitation and care assistant support with specialist rehabilitation alone and usual care for people with Parkinson's living in the community: study protocol for a randomised controlled trial\", 'Collaborative community based care for people and their families living with schizophrenia in India: protocol for a randomised controlled trial')\n",
        "(2386, u'http://dx.doi.org/10.1186/1532-429x-12-s1-o32', u'Development and validation of 3 Tesla functional cardiac magnetic resonance imaging in preterm and term newborns', 'Functional Cardiac Magnetic Resonance Imaging in Preterm and Term Newborns')\n",
        "(2391, u'http://dx.doi.org/10.1136/jme.2010.041111', u'The right not to know: the case of psychiatric disorders', 'The right not to know the case of psychiatric disorders')\n",
        "(2410, u'http://dx.doi.org/10.1242/dev.046797', u'Interdependence of macrophage migration and ventral nerve cord development in Drosophila embryos', 'Ena drives invasive macrophage migration in Drosophila embryos')\n",
        "(2416, u'http://dx.doi.org/10.1242/jcs.083485', u'Phospholipase C\\xa0 binding to PtdIns(4,5)P2 requires the XY-linker region', 'Phospholipase C zeta binding to PIP2 requires the XY linker region')\n",
        "(2466, u'http://dx.doi.org/10.1016/0309-1651(81)90138-7', u'There is a common structural basis for particle binding, cell adhesion and aggregation in', 'STRUCTURAL BASIS OF THE 9 FOLD')\n",
        "(2530, u'http://dx.doi.org/10.1016/j.yexcr.2012.08.003', u'Concanavalin-A triggers inflammatory response through JAK/STAT3 signalling and modulates MT1-MMP regulation of COX-2 in mesenchymal stromal cells', 'Strucuture, function and regulation of JLP signalling complexes ion neugenes')\n",
        "(2533, u'http://dx.doi.org/10.1016/0014-5793(80)80317-6', u'Electron microscopy study of fibronectin structure', 'Insights into the structure of the CCR4-NOT complex by electron microscopy')\n",
        "(2550, u'http://dx.doi.org/10.1097/00004583-199704000-00014', u'Inattentive and Hyperactive Behaviors and Driving Offenses in Adolescence', 'Links between co-occurring social-communication and hyperactive-inattentive trait trajectories')\n",
        "(2590, u'http://dx.doi.org/10.1097/00004583-199909000-00017', u'Symptoms of Depression in Adolescents With Epilepsy', 'Investigating environmental  links between maternal depression symptoms and child anxiety/depression symptoms using a genetic design; the effects of shared adversity..')\n",
        "(2594, u'http://dx.doi.org/10.1016/s0140-6736(10)61457-2', u\"Effect of single-dose anthelmintic treatment during pregnancy on an infant's response to immunisation and on susceptibility to infectious diseases in infancy: a randomised, double-blind, placebo-controlled trial\", 'Effect of single-dose anthelmintic treatment during pregnancy ')\n",
        "(2629, u'http://dx.doi.org/10.1016/j.nbd.2010.08.005', u'Does gene deletion of AMPA GluA1 phenocopy features of schizoaffective disorder?', 'Does gene deletion of AMPA GluA 1 phenococopy features of schizoaffective disorder?')\n",
        "(2671, u'http://dx.doi.org/10.1016/j.neuroimage.2011.03.070', u'Diffusion imaging of whole, post-mortem human brains on a clinical MRI scanner', 'Diffusion imaging of whole, post-mortem himan brains on a clinical MRI scanner')\n",
        "(2701, u'http://dx.doi.org/10.1016/j.neulet.2010.08.074', u'The trafficking of NaV1.8', 'The trafficking of Na(V)1.8')\n",
        "(2703, u'http://dx.doi.org/10.1016/j.ophtha.2011.03.016', u'Inverse Association of Vitamin C with Cataract in Older People in India', 'Inverse association of vitaimin C with cataract in older people in India')\n",
        "(2708, u'http://dx.doi.org/10.1016/j.pain.2010.12.028', u'Transcriptional repression of the M channel subunit Kv7.2 in chronic nerve injury', 'Transcriptional Repression of the M Chanell Subunit Kv7.2 in Chronic Nerve Injury')\n",
        "(2719, u'http://dx.doi.org/10.1016/j.resmic.2010.09.005', u'Expression and localization of SpoIISA toxin during the life cycle of Bacillus subtilis', 'Expression and localization of SpollSA toxin during the life cycle of Bacillus subtillis')\n",
        "(2779, u'http://dx.doi.org/10.3324/haematol.2010.028167', u'Nutritional status, hospitalization and mortality among patients with sickle cell anemia in Tanzania', 'Nutritional status, hospitalization and mortality among patients with ...- page charge')\n",
        "(2790, u'http://dx.doi.org/10.4155/fmc.10.282', u'Crystal structures of 11\\u03b2-hydroxysteroid dehydrogenase type 1 and their use in drug discovery', 'The crystal structures of 11 beta hydroxysteroid dehydrogenase and their use in drug discovery')\n",
        "(2799, u'http://dx.doi.org/10.1016/b978-0-12-374462-3.00001-0', u'Understanding Psychological Trauma and Posttraumatic Stress Disorder (PTSD)', 'Understanding and treating unwanted trauma memories in posttraumatic stress disorder')\n",
        "(2801, u'http://dx.doi.org/10.1097/00001648-199905000-00022', u'The Effects of Environmental Tobacco Smoke Exposure on Lung Function in a Longitudinal Study of British Adults', 'Wood smoke exposure, poverty and impaired lung function in Malwaian adults')\n",
        "(2804, u'http://dx.doi.org/10.1107/s1744309110027600', u'A new crystal form of Lys48-linked diubiquitin', 'A NEW CRYSTAL FORM OF LYS48-LINKED DIUBIQUITIN')\n",
        "(2808, u'http://dx.doi.org/10.1186/1750-1326-6-5', u\"MyD88-adaptor protein acts as a preventive mechanism for memory deficits in a mouse model of Alzheimer's disease\", 'Expression of the neuronal adaptor protein X11alpha protects against memory dysfunction in a transgenic mouse model of Alzheimers disease')\n",
        "(2809, u'http://dx.doi.org/10.1074/jbc.m100175200', u\"Alzheimer's Disease Amyloid-beta Binds Copper and Zinc to Generate an Allosterically Ordered Membrane-penetrating Structure Containing Superoxide Dismutase-like Subunits\", 'Deficiency of the Copper Chaperone for Superoxide Dismutase Increases Amyloid-beta Production')\n",
        "(2816, u'http://dx.doi.org/10.3791/2609', u'Measuring Motor Coordination in Mice', 'Measuring motor coordination in mice')\n",
        "(2818, u'http://dx.doi.org/10.3791/2693', u'Invasion of Human Cells by a Bacterial Pathogen', 'Invasion of human cells by a bacterial pathogen.')\n",
        "(2839, u'http://dx.doi.org/10.1101/gad.615211', u'Nuclear actin polymerization is required for transcriptional reprogramming of Oct4 by oocytes', 'Nuclear actin and transcriptional activation.  Published as an addendum to Nuclear actin polymerization is required\\nfor transcriptional reprogramming of Oct4\\nby oocytes. Genes Dev 2011; 25:94658;\\nPMID: 21536734')\n",
        "(2848, u'http://dx.doi.org/10.1089/ten.tec.2011.0347', u'Development of Methods for Studying the Differentiation of Human Mesenchymal Stem Cells Under Cyclic Compressive Strain', 'Development of methods for studying the differentation of hMSC under cylic compressive strain')\n",
        "(2850, u'http://dx.doi.org/10.3390/ijms12010588', u'Phospholipases A1', 'Phospholipases A1')\n",
        "(2853, u'http://dx.doi.org/10.1073/pnas.1007518107', u'Sequence-specific assembly of FtsK hexamers establishes directional translocation on DNA', 'KOPS DEPENDENT ASSEMBLY OF FTSK HEXAMERS ESTABLISHERS DIRECTIONAL TRANSLOCATION ON DNA')\n",
        "(2858, u'http://dx.doi.org/10.1073/pnas.1009396107', u'Serotonin selectively influences moral judgment and behavior through effects on harm aversion', 'Serotonin selectively influences moral judgement and behaviour through effects on harm aversion')\n",
        "(2859, u'http://dx.doi.org/10.1073/pnas.1003421107', u\"Ubiquitination of lysine-331 by Kaposi's sarcoma-associated herpesvirus protein K5 targets HFE for lysosomal degradation\", 'Ubiquitination of lysine-331 by KSHV protein K5 targets HFE for lysosomal degredation')\n",
        "(2860, u'http://dx.doi.org/10.1073/pnas.1100186108', u'Bacterial persistence by RNA endonucleases', 'Bacterial persistance by RNA endonucleases')\n",
        "(2862, u'http://dx.doi.org/10.1073/pnas.1101748108', u'Targeting of mannan-binding lectin-associated serine protease-2 confers protection from myocardial and gastrointestinal ischemia/reperfusion injury', 'Targetting of Masp2 confers protection from myocardial gastrointestinal inschemia/reperfusion injury')\n",
        "(2866, u'http://dx.doi.org/10.1073/pnas.1019496108', u'The dominantly expressed class I molecule of the chicken MHC is explained by coevolution with the polymorphic peptide transporter (TAP) genes', 'The dominantly-expressed class I molecule of the chicken MHC is explained by the co-evolution with polymorphic TAPs')\n",
        "(2867, u'http://dx.doi.org/10.1073/pnas.1102690108', u'Correction for Aley et al., Nicotinic acid adenine dinucleotide phosphate regulates skeletal muscle differentiation via action at two-pore channels', 'NAADP regulates skeletal muscle differentiation via action at Two-Pore ChannelsQ1')\n",
        "(2876, u'http://dx.doi.org/10.1038/sj.leu.2405056', u'T-cell lymphomas in T-cell-specific Pten-deficient mice originate in the thymus', 'Effect of PI3K- and mTOR-specific inhibitors on spontaneous B-cell follicular lymphomas in PTEN/LKB1-deficient mice.\\n')\n",
        "(2877, u'http://dx.doi.org/10.1038/cddis.2011.54', u'Ocular neuroprotection by siRNA targeting caspase-2', 'Ocular neuroprotection by eIRNA targetting caspase-2')\n",
        "(2893, u'http://dx.doi.org/10.1038/eye.2011.175', u'Evaluation of early and late presentation of patients with ocular mucous membrane pemphigoid to two major tertiary referral hospitals in the United Kingdom', 'Evaluation of early and late presentation of patients with OTMM')\n",
        "(2910, u'http://dx.doi.org/10.1093/aje/kwr053', u'Association Between Urban Life-Years and Cardiometabolic Risk: The Indian Migration Study', 'Association between Urban Life-Years and Cardio-Metabolic Risk')\n",
        "(2911, u'http://dx.doi.org/10.1093/bioinformatics/btr304', u'Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA', 'Java Bioinformtics Analysis Web Services for Multiple Sequence alignment - JABAWS:MSA')\n",
        "(2914, u'http://dx.doi.org/10.1093/brain/awr170', u\"A randomized placebo-controlled trial of idebenone in Leber's hereditary optic neuropathy\", 'A randomized placebo-controlled trial of ibernone in Lebers hereditary optic nuropathy')\n",
        "(2917, u'http://dx.doi.org/10.1016/s0022-510x(05)80577-5', u'0205 A novel OPA1 mutation in a family with autosomal dominant optic atrophy', 'Reply: Spatic paraplegia in dominant optic plus pehnotype due to OPA1 mutation')\n",
        "(2932, u'http://dx.doi.org/10.1093/cvr/cvq305', u'Potent suppression of vascular smooth muscle cell migration and human neointimal hyperplasia by KV1.3 channel blockers', 'Potent suppression of vascular smooth cenn migration and human neontimal hyperplasia by KV1.3 channel blockers')\n",
        "(2952, u'http://dx.doi.org/10.1093/eurpub/ckq030', u'Alcohol policy in a Russian region: a stakeholder analysis', 'Alcohol policy in a Russian region.')\n",
        "(2955, u'http://dx.doi.org/10.1093/glycob/cwq173', u'Biochemical characterization of the Mycobacterium tuberculosis phosphoribosyl-1-pyrophosphate synthetase', 'Biochemical characterisation of the Mycobacterium tuberculosis phosphoribosyl-1-pyophosphate synthetase (Mt-PrsA)')\n",
        "(2984, u'http://dx.doi.org/10.1093/infdis/jir512', u'The Human Transcriptome During Nontyphoid Salmonella and HIV Coinfection Reveals Attenuated NF\\xa0B-Mediated Inflammation and Persistent Cell Cycle Disruption', 'The human transcriptome during non-typhoid salmonella and HIV co-infection')\n",
        "(3024, u'http://dx.doi.org/10.1093/nar/gkr085', u'Sam68 marks the transcriptionally active stages of spermatogenesis and modulates alternative splicing in male germ cells', 'Analysis of the molecular mechanisms which activate alternative pre-mRNA splicing pathways in germ cells and repress these splicing events in germ cells')\n",
        "(3049, u'http://dx.doi.org/10.1006/dbio.1998.9031', u'Retinal Neurogenesis: The Formation of the Initial Central Patch of Postmitotic Cells', 'T-cells and neurogenesis')\n",
        "(3056, u'http://dx.doi.org/10.1371/journal.pcbi.1000981', u'Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes', 'Quantifying the impact of HIV-1 escape from CTLs')\n",
        "(3060, u'http://dx.doi.org/10.1371/journal.pgen.1002105', u'Multiple Common Susceptibility Variants near BMP Pathway Loci GREM1, BMP4, and BMP2 Explain Part of the Missing Heritability of Colorectal Cancer', 'Multiple common susceptibility varients near BMP pathway loci GREM1 BMP4 and BMP2')\n",
        "(3121, u'http://dx.doi.org/10.1371/journal.pone.0018899', u'Staphylococcus aureus Keratinocyte Invasion Is Dependent upon Multiple High-Affinity Fibronectin-Binding Repeats within FnBPA', 'Staphylococcus aureus Keratinocyte Invasion is Dependent upon Multiple High-affinity Fibronectin-Bin; Article no: PONE-D-11-00228')\n",
        "(3152, u'http://dx.doi.org/10.1371/journal.pone.0008894', u'Alpha-1,2-Mannosidase and Hence N-Glycosylation Are Required for Regulatory T Cell Migration and Allograft Tolerance in Mice', 'Alpha-1,2-Mannosidase and Treg')\n",
        "(3165, u'http://dx.doi.org/10.1371/journal.pone.0008068', u'Pathway Analysis of GWAS Provides New Insights into Genetic Susceptibility to 3 Inflammatory Diseases', 'Pathway analysis of AD GWAS')\n",
        "(3166, u'http://dx.doi.org/10.1371/journal.pone.0091270', u'Correction: The Role of Matrix Metalloproteinase in the Intimal Sarcoma-Like Cells Derived from Endarterectomized Tissues from a Chronic Thromboembolic Pulmonary Hypertension Patient', 'PPAR in pulmonary hypertension')\n",
        "(3167, u'http://dx.doi.org/10.1371/journal.pone.0022179', u'Prevalence and Predictors of Vitamin D Insufficiency in Children: A Great Britain Population Based Study', 'Prevalence and predictors of vitimin D')\n",
        "(3170, u'http://dx.doi.org/10.1371/journal.pone.0017017', u'Tumor Suppressor RASSF1A Promoter: p53 Binding and Methylation', 'SGK1 promoter methylation')\n",
        "(3171, u'http://dx.doi.org/10.1371/journal.pone.0017765', u'Ten Years of Surveillance for Invasive Streptococcus pneumoniae during the Era of Antiretroviral Scale-Up and Cotrimoxazole Prophylaxis in Malawi', 'Ten years of surveillance for Invasive Streptococcus pneumoniae during the era of anliretroviral sca')\n",
        "(3186, u'http://dx.doi.org/10.1371/journal.ppat.1003953', u'Mycobacteriophages: Windows into Tuberculosis', 'Rv1986 of M. tuberculosis')\n",
        "(3194, u'http://dx.doi.org/10.1002/0471650129.dob0054', u\"Bayesian Analysis (Bayes' Theorem)\", 'Bayesian multi-tissue analysis')\n",
        "(3197, u'http://dx.doi.org/10.1042/bj20101581', u' Divergent effect of mammalian PLC\\u03b6 in generating Ca 2+ oscillations in somatic cells compared with eggs ', 'Divergent of mammalian PLC-zeta in generating Ca2+ oscillations in somatic cels versus eggs')\n",
        "(3206, u'http://dx.doi.org/10.1042/bj20101593', u'How the biotin\\u2013streptavidin interaction was made even stronger: investigation via crystallography and a chimaeric tetramer', 'HOW THE BIOTIN-STRETAVDIN INTERACTION WAS MADE EVEN STRONGER')\n",
        "(3212, u'http://dx.doi.org/10.1192/bjp.bp.111.092130', u'Clinical and cognitive characteristics of children with attention-deficit hyperactivity disorder, with and without copy number variants', 'Clinical and cognitive characteristics of ADHD children with and without copy number variants')\n",
        "(3213, u'http://dx.doi.org/10.1192/bjp.bp.110.087866', u'Polygenic dissection of the bipolar phenotype', 'Polygenic dissection of the bipolar phenotype')\n",
        "(3214, u'http://dx.doi.org/10.4314/njpsyc.v7i1.53921', u'A new movement for global mental health and its possible impact in Nigeria', 'The movement for global mental health')\n",
        "(3218, u'http://dx.doi.org/10.1192/bjp.bp.110.078741', u'Prevalence of bipolar disorder in children and adolescents with attention-deficit hyperactivity disorder', 'Does bipolar disorder commonly occur in children and adolescents with  attention deficit hyperactivity disorder?  A UK study')\n",
        "(3220, u'http://dx.doi.org/10.1192/bjp.bp.111.092155', u'Lay health worker led intervention for depressive and anxiety disorders in India: impact on clinical and disability outcomes over 12 months', 'The effectiveness of a lay health worker led collaborative stepped care intervnetion for depressive and anxiety disorders ....')\n",
        "(3224, u'http://dx.doi.org/10.1098/rsbl.2009.0360', u'Pitch then power: limitations to acceleration in quadrupeds', 'Pitch then Power: limitations to accelerator in accelerator')\n",
        "(3241, u'http://dx.doi.org/10.1258/shorts.2010.010079', u'Rheumatoid corneal melt: autoimmunity or infection?', 'Rheumatoid Corneal Melt: Autoimmunity or Infection?')\n",
        "(3311, u'http://dx.doi.org/10.1007/s10519-010-9424-3', u'Investigation of Dyslexia and SLI Risk Variants in Reading- and Language-Impaired Subjects', 'Dyslexia / SLI Variants')\n",
        "(3333, u'http://dx.doi.org/10.1080/17530350.2011.535329', u'INTRODUCTION', 'Intro: The value of transnational medical research')\n",
        "(3378, u'http://dx.doi.org/10.1002/cmdc.201100144', u'Discovery of Adamantyl Heterocyclic Ketones as Potent 11\\u03b2-Hydroxysteroid Dehydrogenase Type 1 Inhibitors', 'Discovery of adamantyl heterocyclic ketones as potent human cellular\\n11_-hydroxysteroid dehydrogenase type 1 inhbitors, Manuscript: 201100144')\n",
        "(3386, u'http://dx.doi.org/10.1111/j.1467-7687.2010.00990.x', u'Is auditory discrimination mature by middle childhood? A study using time-frequency analysis of mismatch responses from 7 years to adulthood', 'IS AUDITORY DISCRIMINATION MATURE BY MIDDLE CHILDHOOD?')\n",
        "(3409, u'http://dx.doi.org/10.1107/s0108270109032004/gz3168sup1.cif', None, 'Crystal Structure of Onconasi at I.IA')\n",
        "(3410, u'http://dx.doi.org/10.1016/0014-5793(79)80516-5', u'Structural characterization of seven different subunits in Androctonus australis haemocyanin', 'Structural Characterization of angiotousin')\n",
        "(3417, u'http://dx.doi.org/10.1111/j.1601-183x.2011.00703.x', u'Gene-environment interactions between CRHR1 variants and physical assault in suicide attempts', 'Additional page charges for Vol 10 Issue 3 Manuscript no. 672')\n",
        "(3461, u'http://dx.doi.org/10.1111/j.1365-2958.2011.07640.x', u'Lipoarabinomannan biosynthesis in Corynebacterineae: the interplay of two \\u03b1(1\\u21922)-mannopyranosyltransferases MptC and MptD in mannan branching', 'Lipoarbinomannan biosynthesis in Corynebacterineae.')\n",
        "(3484, u'http://dx.doi.org/10.1021/cb200292c', u'A Multifunctional Protease Inhibitor To Regulate Endolysosomal Function', 'A multi-functional proteaage inhibitor to regulate endo-lysomal function')\n",
        "(3488, u'http://dx.doi.org/10.1021/ac300815c', u'Toggled RNA Aptamers Against Aminoglycosides Allowing Facile Detection of Antibiotics Using Gold Nanoparticle Assays', 'Toggled RNA aptamers against aminologlycosides allow facile direction of antibiotics using gold nanpartical assays')\n",
        "(3501, u'http://dx.doi.org/10.1021/ja9029768', u'Inhibitory Substrate Binding Site of Human Indoleamine 2,3-Dioxygenase', 'The mechanism of substrate inhibilitation in human indoleamine 2,3 dioxygenase')\n",
        "(3538, u'http://dx.doi.org/10.1037/a0025297', u'Jumping to conclusions, a lack of belief flexibility and delusional conviction in psychosis: A longitudinal investigation of the structure, frequency, and relatedness of reasoning biases.', 'Delusional conviction and reasoning biases: change and relationships over time.')\n",
        "(3542, u'http://dx.doi.org/10.1037/0278-7393.22.6.1494', u'Sentential context effects on lexical decisions with a cross-modal instead of an all-visual procedure.', 'Context-Gated Statistical Learning and Its Role in Visual-Saccadic Decisions')\n",
        "(3588, u'http://dx.doi.org/10.1074/jbc.m111.289488', u'A Single Autoimmune T Cell Receptor Recognizes More Than a Million Different Peptides', 'A single autoimmune T-cell receptor recognizes over a million different peptides.  Article number 9305')\n",
        "(3598, u'http://dx.doi.org/10.1074/jbc.m111.324988', u'Monocyte-to-Macrophage Differentiation: SYNTHESIS AND SECRETION OF A COMPLEX EXTRACELLULAR MATRIX', 'Monocyte to macrophage differentiation: synthesis and secretion of novel extraceullar matrix components')\n",
        "(3609, u'http://dx.doi.org/10.1074/jbc.m111.317990', u'A Conserved Function for the H2A.Z C Terminus', 'A conserved function for the H2A.Z C terminus')\n",
        "(3621, u'http://dx.doi.org/10.1091/mbc.e11-08-0694', u'A VE-cadherin-PAR3-\\xa0-catenin complex regulates the Golgi localization and activity of cytosolic phospholipase A2\\xa0 in endothelial cells', 'A VE-cadherin-PAR3-a-catenin complex reculates the Golgi localization and activity of cytrosolic phosppholipase A2a in enothelial cells')\n",
        "(3651, u'http://dx.doi.org/10.5720/kjcn.2012.17.2.156', u'Development and Evaluation of the Semi-quantitative Food Frequency Questionnaire to Assess Folate Intake in Women of Child-bearing Age', 'Development and evaluation of a semi-quantitative food frequency questionnaire for use in urban and rural India.')\n",
        "(3698, u'http://dx.doi.org/10.1186/1471-2164-13-106', u'Quantitative genome re-sequencing defines multiple mutations conferring chloroquine resistance in rodent malaria', 'Quantitative Genome re-sequencing defines multiple mutations conferrin')\n",
        "(3714, u'http://dx.doi.org/10.1186/1866-1955-4-23', u'Fragile X syndrome: a pilot proton magnetic resonance spectroscopy study in premutation carriers', 'Fragile X Syndrome. A pilot Proton Magnetic Resonance Spectroscopy Study of glutamate metabolism and neuronal integrity in Pre-mutation carriers.')\n",
        "(3743, u'http://dx.doi.org/10.1186/1758-907x-3-8', u'MicroRNAs from the same precursor have different targeting properties', 'MicroRNA from the same precurser have different target')\n",
        "(3755, u'http://dx.doi.org/10.1136/archdischild-2012-301882', u'Family-based association study of ADHD and genes increasing the risk for smoking behaviours', 'Family based association study of ADHD and genes increasing the risk of smoking behaviours')\n",
        "(3757, u'http://dx.doi.org/10.1136/bmj.d7373', u'Compliance with mandatory reporting of clinical trial results on ClinicalTrials.gov: cross sectional study', 'Compliance with mandotory reporting of clinical trial results on ClincalTrials.gov - a cross sectional study')\n",
        "(3819, u'http://dx.doi.org/10.1083/jcb.200307070', u'Chromosome instability in colorectal tumor cells is associated with defects in microtubule plus-end attachments caused by a dominant mutation in APC', 'Tumourigenic fragments of APC cause dominant defects in directional cell migration in multiple model systems.')\n",
        "(3838, u'http://dx.doi.org/10.1016/j.ajhg.2014.03.004', u'Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits', 'Genome-wide association studies in partial epilepsies')\n",
        "(3841, u'http://dx.doi.org/10.1016/j.brat.2009.01.019', u'Mindfulness-based cognitive therapy as a treatment for chronic depression: A preliminary study', 'Mindfulness-based cognitive therapy as a treatment for chronic depression : a prelimary study')\n",
        "(3843, u'http://dx.doi.org/10.1016/j.brat.2010.03.008', u'Testing a new cognitive behavioural treatment for obesity: A randomized controlled trial with three-year follow-up', 'Testing a new cognitive behavioural treatment for obesity:  A randomiized controlled trial with three-year follow-up')\n",
        "(3844, u'http://dx.doi.org/10.1016/j.brat.2009.10.008', u'The significance of overvaluation of shape and weight in binge eating disorder', 'The significance and overevaluation of shape and weight in binge eating disorder')\n",
        "(3995, u'http://dx.doi.org/10.1016/j.jad.2011.06.046', u'The impact of educational status on the clinical features of major depressive disorder among Chinese women', 'The Impact of Educational Status on the Clinical Features of Major Depressive Disorder Among Chinese Women. JAD5137')\n",
        "(4017, u'http://dx.doi.org/10.1016/j.jneumeth.2011.05.011', u'An automated calibration method for non-see-through head mounted displays', 'An automated calibration method for non-see-through head mounted displays     http://dx.doi.org/10.1016/j.jneumeth.2011.05.011')\n",
        "(4018, u'http://dx.doi.org/10.1016/j.jneumeth.2011.01.026', u\"Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease\", \"Detection of early locomotor abnormalities in a Drosophila model of Alzheimer's disease by a three-dimensional tracking system\")\n",
        "(4027, u'http://dx.doi.org/10.1097/chi.0b013e3181a8136d', u'Risk Factors for Full- and Partial-Syndrome Early Adolescent Eating Disorders: A Population-Based Pregnancy Cohort Study', 'Prevalence of Tourettes syndrome and chronic tics in the population-based ALSPAC cohort')\n",
        "(4029, u'http://dx.doi.org/10.1016/s0090-4295(01)01258-4', u'Massive extracellular tryptase from activated bladder mast cells in interstitial cystitis', 'Morphological and Physiological Characterisation of interstitial Cells from the urinary bladder')\n",
        "(4194, u'http://dx.doi.org/10.3389/fnhum.2011.00062', u'Specialization in the Human Brain: The Case of Numbers', 'Specialisation in the human brain: the case of numbers')\n",
        "(4245, u'http://dx.doi.org/10.3791/3381', u'Electroporation of Craniofacial Mesenchyme', ' Electroporation of craniofacial mesenchyme.')\n",
        "(4271, u'http://dx.doi.org/10.1073/pnas.1119326109', u'Designing biomimetic pores based on carbon nanotubes', 'DESIGNING BIOMIMETIC PORES BASED ON CARBON NANOTUBES')\n",
        "(4272, u'http://dx.doi.org/10.1073/pnas.1110270109', u'Structural basis for DNA recognition and loading into a viral packaging motor', 'Structural basis for DNA recognition and loading into a viral packaging motor')\n",
        "(4275, u'http://dx.doi.org/10.1073/pnas.1109173109', u'A tolerogenic role for Toll-like receptor 9 is revealed by B-cell interaction with DNA complexes expressed on apoptotic cells', 'A tolerogenic role for TLR9 is revelaed by B cell interaction with DNA expressed on apoptotic cells')\n",
        "(4277, u'http://dx.doi.org/10.1073/pnas.1201872109', u'Agonist binding evokes extensive conformational changes in the extracellular domain of the ATP-gated human P2X1 receptor ion channel', 'Agonist binding evokes extensive conformational charges; the extracellular domain of the AIP gated human px21 receptor ion chanel')\n",
        "(4279, u'http://dx.doi.org/10.1073/pnas.1116981109', u'Mechanisms contributing to central excitability changes during hearing loss', 'Mechanisms contributing to the central excitability changes during hearing losss.')\n",
        "(4290, u'http://dx.doi.org/10.1073/pnas.1113195108', u'A common visual metric for approximate number and density', 'A common visual metric for approximate number and density')\n",
        "(4293, u'http://dx.doi.org/10.1073/pnas.1115861108', u'High-resolution human cytomegalovirus transcriptome', 'High-resolution human cytomegalovirus transcriptome')\n",
        "(4302, u'http://dx.doi.org/10.1073/pnas.1205651109', u'Generation of quinolone antimalarials targeting the Plasmodium falciparum mitochondrial respiratory chain for the treatment and prophylaxis of malaria', 'Generation of quinolone antimalarials targeting the Plasmodium faciparum mitochondrial respiratory chain for the treatment and prophylaxis of malaria')\n",
        "(4315, u'http://dx.doi.org/10.1038/emboj.2012.151', u' Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae ', 'Pex 3 - anchored ATG 36 tags peroxissiomes for degredation in saccharomyes cerevisial')\n",
        "(4325, u'http://dx.doi.org/10.1007/springerreference_84057', u'Population Genetics and Human Health', 'Behavioural genetics and population health intervention.')\n",
        "(4387, u'http://dx.doi.org/10.1093/cvr/cvq346', u'Soluble FLT1 sensitizes endothelial cells to inflammatory cytokines by antagonizing VEGF receptor-mediated signalling', 'Soluble FLT-1 sensitises endothelial cells to inflammatory Cytokines')\n",
        "(4419, u'http://dx.doi.org/10.1093/hmg/ddq469', u\"Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21\", \"Dissection of the genetics of Parkinsons disease (pubd as Dissection of the genetics of Parkinson's disease identifies an additional association 5' of SNCA and multiple associated haplotypes at 17q21.)\")\n",
        "(4425, u'http://dx.doi.org/10.1093/infdis/jir466', u'Changes in Serogroup and Genotype Prevalence Among Carried Meningococci in the United Kingdom During Vaccine Implementation', 'Changes in serogroup and genotype prevalence among carried meningococi in the United Kingdom during vaccine implementation')\n",
        "(4481, u'http://dx.doi.org/10.1042/bj20110912', u' Translation of a minigene in the 5\\u2032 leader sequence of the enterohaemorrhagic Escherichia coli LEE1 transcription unit affects expression of the neighbouring downstream gene ', 'Translation of minigene in the 5 leader sequence of the enterhaemorrhagic')\n",
        "(4554, u'http://dx.doi.org/10.1371/journal.pone.0027760', u'Exploring Mechanisms of Multiple Insecticide Resistance in a Population of the Malaria Vector Anopheles funestus in Benin', 'Exploring mechanisims of multiple insecticide resistance in apopulation of the malaria vector Anophe')\n",
        "(4576, u'http://dx.doi.org/10.1371/journal.pone.0041923', u'Mycobacterium tuberculosis Complex Lipid Virulence Factors Preserved in the 17,000-Year-Old Skeleton of an Extinct Bison, Bison antiquus', 'Mycobacterium tuberculois complex lipid virulence')\n",
        "(4577, u'http://dx.doi.org/10.1371/journal.pone.0034813', u'Neuropathology of 16p13.11 Deletion in Epilepsy', 'Neuropathology of 16p13.11 Deletion in Epilepsy')\n",
        "(4588, u'http://dx.doi.org/10.1371/journal.pone.0030095', u'T-Cell Responses to the DBL\\u03b1-Tag, a Short Semi-Conserved Region of the Plasmodium falciparum Membrane Erythrocyte Protein 1', 'T-cell Responses to the DBLa-tag a Short Semi-conseved Region of the Plasmodium falciparum membrane')\n",
        "(4697, u'http://dx.doi.org/10.1371/journal.pone.0050325', u'Impact of Anthelminthic Treatment in Pregnancy and Childhood on Immunisations, Infections and Eczema in Childhood: A Randomised Controlled Trial', 'Impact of anthelminthic treatment in pregnancy and early childhood on response to immunisation and on the ....')\n",
        "(4713, u'http://dx.doi.org/10.1016/j.molbiopara.2009.03.006', u'Dysregulation of coagulation in cerebral malaria', 'Dysregulation of coagulation in cerebral malaria')\n",
        "(4714, u'http://dx.doi.org/10.5772/52668', u'Coupled Enzyme Activity and Thermal Shift Screening of the Maybridge Rule of 3 Fragment Library Against Trypanosoma brucei Choline Kinase; A Genetically Validated Drug Target', 'Validating Choline Metabolism as a drug target in the fight against T. brucei')\n",
        "(4720, u'http://dx.doi.org/10.1192/bjp.bp.111.094896', u'Psychosis incidence through the prism of early intervention services', 'Psychosis incidence through the prism of early intervention services: Initial findings from the SEPEA study')\n",
        "(4756, u'http://dx.doi.org/10.1243/pime_proc_1987_201_115_02', u'A Parameter Sensitivity Analysis for the Dynamic Model of a Variable Displacement Axial Piston Pump', 'The Sensitivity of a Lower Limb Model to Axial Rotation Offsets and Muscle Bounds at the Knee')\n",
        "(4790, u'http://dx.doi.org/10.1523/jneurosci.0082-12.2012', u'Navigating the Auditory Scene: An Expert Role for the Hippocampus', 'Navigating the auditory scene - an expert role for the hippocamus')\n",
        "(4791, u'http://dx.doi.org/10.1080/000155500750043113', u'Dermatoscopic Diagnosis of Malignant Melanoma', 'Novice identification of melanoma: not quite as straightforward as the ABCDs.')\n",
        "(4805, u'http://dx.doi.org/10.1074/jbc.m805963200', u'Control of Periplasmic Interdomain Thiol:Disulfide Exchange in the Transmembrane Oxidoreductase DsbD', 'Control of Periplasmic Interdomain Thiol:Disulfide Exchange in the Transmembrane Oxidoreductase DsbD\\n')\n",
        "(4945, u'http://dx.doi.org/10.1002/aur.185', u'Commentary for Special Issue of Autism Research on Mouse Models in ASD: A Clinical Perspective', 'Special Issue: Global Perspectives on Autism (Issue edited by M Elsabbagh + she published 3 articles in issue)')\n",
        "(4965, u'http://dx.doi.org/10.1002/cmdc.201100420', u'Design, Synthesis and Biological Evaluation of Trypanosoma brucei Trypanothione Synthetase Inhibitors', 'Design, synthesis and biological evaluation of novel trypansomoa brucei Trypanothion Synthetase inhibitors')\n",
        "(5012, u'http://dx.doi.org/10.1002/hep.24263', u'Estimating the net contribution of interleukin-28B variation to spontaneous hepatitis C virus clearance', 'Estimating the Net Contribution of Interleaking-28B Variation to Spotaneous Hepatitis C Virus Clearence')\n",
        "(5024, u'http://dx.doi.org/10.1002/jbmr.399', u'Signal peptide mutations in RANK prevent downstream activation of NF-\\u03baB', 'Signal Peptide Mutations in RANK Prevent Downstream Activation of NF-_B')\n",
        "(5033, u'http://dx.doi.org/10.1111/j.1469-7610.2011.02495.x', u'Annual Research Review: The nature and classification of reading disorders - a commentary on proposals for DSM-5', 'The Nature, Causes and Classification of Reading Disorders: Implications for DSM-V (JCCP reference number 2011-00070 RI)')\n",
        "(5051, u'http://dx.doi.org/10.1097/00132985-200511000-00001', u'CORTICAL STIMULATION IMPROVES ARM, HAND FUNCTION AFTER STROKE', 'Assessment of cortical reorganisation for hand function after stroke')\n",
        "(5791, u'http://dx.doi.org/10.11646/zootaxa.3637.2.4', u'Three new species of the genus <i>Suctobelbella</i> (Acari: Oribatida: Suctobelbidae) from Sanjiang Plain, Northeast China', 'First record of the littoral genus Alismobates (Acari: Oribatida) from the Atlantic ocean, with a redefinition of the family Fortuyniidae based on adult and juvenile morphology.')\n"
       ]
      }
     ],
     "prompt_number": 70
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Because I didn't clean up the journal names in the new Wellcome Trust data there are correct matches that haven't been caught in this sieve so I will add them to the fixed set. Then the new set of DOIs are then incorporated into the full data set. The article titles are not corrected so they can be compared later."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "indices = [2095, 2098, 2148, 2149, 2177, 2230, 2244, 2304, 2391, 2416, 2594, 2629, 2671, 2701, 2703, 2708, 2719, 2779, 2790, 2799, 2804, 2816, 2848, 2858, 2859, 2860, 2862, 2866, 2867, 2877, 2893, 2910, 2911, 2914, 2932, 2952, 2955, 2984, 3056, 3060, 3121, 3171, 3197, 3206, 3212, 3213, 3224, 3241, 3378, 3386, 3461, 3484, 3488, 3501, 3588, 3598, 3609, 3621, 3651, 3698, 3714, 3755, 3757, 3814, 3843, 3844, 3995, 4017, 4018, 4194, 4245, 4271, 4272, 4275, 4277, 4279, 4290, 4293, 4302, 4315, 4387, 4419, 4425, 4481, 4554, 4576, 4577, 4588, 4697, 4713, 4720, 4790, 4805, 4965, 5012, 5024, 5033]\n",
      "\n",
      "for nf in notfixed:\n",
      "    if nf[0] in indices:\n",
      "        fixed.append(nf)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 71
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "len(fixed)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 72,
       "text": [
        "3039"
       ]
      }
     ],
     "prompt_number": 72
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "for fix in fixed:\n",
      "    articles[fix[0]]['doi'] = fix[1][18:len(fix[1])]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 73
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": [
      "Using OAG to detect licenses\n",
      "----------------------------\n",
      "\n",
      "We're using the Open Article Gauge API to determine how many licenses we can obtain for this set of articles. This requires making a list of the DOIs and then sending them off to OAG. Managing the delays and timeouts to get as much back as possible remains a bit of guess work in terms of populating and getting back answers for this many papers."
     ]
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "oagdois = [article.get('doi') for article in articles if (article.get('doi') and article.get('doi').startswith('10.'))]\n",
      "req = pyoag.Request(oagdois, delay=5, timeoutdelay=600)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "Response Status Code: 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Response Status Code:"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        " 200\n",
        "Successfully obtained OAG response for 6437 of 6457 articles"
       ]
      },
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": [
        "\n"
       ]
      }
     ],
     "prompt_number": 98
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "[article.get('license')[0].get('type') for article in req.response if (article.get('license')[0].get('type') != 'failed-to-obtain-license')]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 99,
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        " u'free-to-read',\n",
        " u'cc-by',\n",
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        " u'free-to-read',\n",
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        " u'cc-by',\n",
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        " u'free-to-read',\n",
        " u'cc-by',\n",
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        " u'free-to-read',\n",
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        " u'cc-by',\n",
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        " u'cc-by',\n",
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        " u'cc-by',\n",
        " u'free-to-read',\n",
        " u'free-to-read',\n",
        " u'free-to-read',\n",
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        " u'cc-by',\n",
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        " u'cc-by',\n",
        " u'cc-by',\n",
        " u'free-to-read',\n",
        " u'cc-by',\n",
        " u'cc-by',\n",
        " u'free-to-read',\n",
        " u'free-to-read',\n",
        " u'cc-nc-nd',\n",
        " u'cc-by',\n",
        " u'free-to-read',\n",
        " u'cc-nc']"
       ]
      }
     ],
     "prompt_number": 99
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "failed = [article for article in articles if article.get('doi') not in [a['identifier'][0]['id'] for a in req.response]]\n",
      "len(failed)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 100,
       "text": [
        "93"
       ]
      }
     ],
     "prompt_number": 100
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "index = {}\n",
      "for i, article in enumerate(articles):\n",
      "    index[article.get('doi', 'no-doi')] = i\n",
      "    \n",
      "for article in req.response:\n",
      "    doi = article.get('identifier')[0]['id']\n",
      "    i = index.get(doi)\n",
      "    if i:\n",
      "        articles[i]['oag_license'] = article.get('license')[0].get('type')\n",
      "        articles[i]['license_url'] = article.get('license')[0].get('provenance').get('source')\n",
      "        articles[i]['provenance'] = article.get('license')[0].get('provenance').get('description').encode('utf-8')\n",
      "    "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 111
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "mappin = {'cc-by' : 'cc-by',\n",
      "          'CC BY' : 'cc-by',\n",
      "          'CC-BY' : 'cc-by',\n",
      "          'CC BY-NC' : 'cc-nc',\n",
      "          'CC-BY-NC' : 'cc-nc',\n",
      "          'CC BY NC' : 'cc-nc',\n",
      "          'CC-BY-NC-ND' : 'cc-nc-nd',\n",
      "          'CC BY-NC-ND' : 'cc-nc-nd',\n",
      "          'CC BY-NC-SA' : 'cc-nc-sa',\n",
      "          'CC-BY-NC-SA' : 'cc-nc-sa',\n",
      "          'Publisher copyright' : 'Publisher copyright',\n",
      "          '' : ''}\n",
      "\n",
      "for article in articles:\n",
      "    article['manual_license'] = mappin.get(article.get('manual_license', ''), 'other')\n",
      "          "
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 112
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "with open('output_data/apc-oag.csv', 'w') as f:\n",
      "    writer  = csv.DictWriter(f, ['doi', 'journal', 'title', 'publisher', 'manual_license', 'manual_status', 'oag_license', 'oag_status', 'license_url', 'provenance', 'source'], extrasaction='ignore')\n",
      "    writer.writeheader()\n",
      "    writer.writerows(articles)"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 114
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [
      "req.response[0]"
     ],
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "metadata": {},
       "output_type": "pyout",
       "prompt_number": 109,
       "text": [
        "{u'id': u'doi:10.1016_j.tins.2013.08.001',\n",
        " u'identifier': [{u'canonical': u'doi:10.1016/j.tins.2013.08.001',\n",
        "   u'id': u'10.1016/j.tins.2013.08.001',\n",
        "   u'type': u'doi'}],\n",
        " u'license': [{u'BY': u'',\n",
        "   u'NC': u'',\n",
        "   u'ND': u'',\n",
        "   u'SA': u'',\n",
        "   u'description': u'',\n",
        "   u'error_message': u'unable to detect licence',\n",
        "   u'jurisdiction': u'',\n",
        "   u'open_access': False,\n",
        "   u'provenance': {u'agent': u'OpenArticleGauge Service/0.2 alpha',\n",
        "    u'category': u'failure',\n",
        "    u'date': u'2014-04-16T19:19:17Z',\n",
        "    u'description': u'a plugin ran and failed to detect a license for this record.  This entry records that the license is therefore unknown',\n",
        "    u'handler': u'generic_string_matcher',\n",
        "    u'handler_version': u'0.1',\n",
        "    u'source': u'',\n",
        "    u'source_size': -1},\n",
        "   u'suggested_solution': u'',\n",
        "   u'title': u'',\n",
        "   u'type': u'failed-to-obtain-license',\n",
        "   u'url': u'',\n",
        "   u'version': u''}]}"
       ]
      }
     ],
     "prompt_number": 109
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": [],
     "language": "python",
     "metadata": {},
     "outputs": []
    }
   ],
   "metadata": {}
  }
 ]
}