The Kitchin Research Group: scopus

Generating an alphabetized list of collaborators from the past five years

Posted February 20, 2016 at 05:03 PM | categories: scopus, python | tags:

Updated February 20, 2016 at 05:24 PM

Almost every proposal I write requires some list of my coauthors from the past several years. Some want the list alphabetized, and some want affiliations too. It has always bothered me to make this list, mostly because it is tedious, and it seems like something that should not be hard to generate. It turns out it is not too hard. I have been developing a Python interface ((https://github.com/jkitchin/scopus )) to Scopus that more or less enables me to script this.

Scopus is not free. You need either a license, or institutional access to use it. Here is the strategy to generate my list of coauthors. First, we need to get the articles for the past 5 years that are mine, and for each paper we get the coauthors. I use my Scopus author id in the query, and then sort the names alphabetically into a table. Then, I use that table as input to a second code block that does an author query in Scopus to get the current affiliations. Here is the code.

from scopus.scopus_api import ScopusAbstract
from scopus.scopus_search import ScopusSearch

s = ScopusSearch('AU-ID(7004212771) AND PUBYEAR > 2010')

coauthors = {}
for eid in s.EIDS:
    ab = ScopusAbstract(eid)
    for au in ab.authors:
        if au.auid not in coauthors and au.auid != '7004212771':
            coauthors[au.auid] = au.indexed_name

return sorted([[auid, name] for auid,name in coauthors.items()], key=lambda x:x[1])

52463103500	Akhade S.A.
6506329719	Albenze E.
36472906200	Alesi W.R.
56963752500	Anna S.L.
56522803500	Boes J.R.
26433085700	Calle-Vallejo F.
54973276000	Chao R.
7201800897	Collins T.J.
54883867200	Curnan M.T.
7003584159	Damodaran K.
55328415000	Demeter E.L.
37005464900	Dsilva C.
18037364800	Egbebi A.
35603120700	Eslick J.C.
56673468200	Fan Q.
24404182600	Frenkel A.I.
35514271900	Gellman A.J.
12803603300	Gerdes K.
54585146800	Gumuslu G.
55569145100	Hallenbeck A.P.
24316829300	Hansen H.A.
56009239000	Hilburg S.L.
55676869000	Hopkinson D.
56674328100	Illes S.M.
23479647900	Inoglu N.G.
6603398169	Jaramillo T.F.
8054222900	Joshi Y.V.
47962378000	Keturakis C.
57056061900	Kondratyuk P.
55391991800	Kondratyuk P.
7006205398	Koper M.T.M.
23004637900	Kusuma V.A.
35787409400	Landon J.
55005205100	Lee A.S.
6701399651	Luebke D.R.
35491189200	Man I.C.
27467500000	Mantripragada H.
55373026900	Mao J.X.
55210428500	Marks A.
27667815700	Martinez J.I.
56071079300	Mehta P.
56673592900	Michael J.D.
55772901000	Miller D.C.
7501599910	Miller J.B.
26032231600	Miller S.D.
35576929100	Morreale B.
55308251800	Munprom R.
14036290400	Myers C.R.
7007042214	Norskov J.K.
24081524800	Nulwala H.B.
56347288000	Petrova R.
7006208748	Pushkarev V.V.
56591664500	Raman S.
7004217247	Resnik K.P.
47962694800	Richard Alesi Jr. W.
9742604300	Rossmeisl J.
7201763336	Rubin E.S.
6602471339	Sabolsky E.M.
7004541416	Salvador P.A.
22981503200	Shi W.
55885836600	Siefert N.S.
25224517700	Su H.-Y.
57016792200	Thirumalai H.
8724572500	Thompson R.L.
8238710700	Vasic R.
37081979100	Versteeg P.
7006804734	Wachs I.E.
6701692232	Washburn N.R.
56542538800	Watkins J.D.
55569461200	Xu Z.
56424861600	Yin C.
56969809500	Zhou X.

It is worth inspecting this list for duplicates. I see at least two duplicates. That is a limitation of almost every indexing service I have seen. Names are hard to disambiguate. I will live with it. Now, we will use another query to get affiliations, and the names. Since we use a sorted list from above, these names are in alphabetical order. We exclude co-authors from Carnegie Mellon University since these are often my students, or colleagues, and they are obvious conflicts of interest for proposal reviewing anyway. I split the current affiliation on a comma, since it appears the institution comes first, followed by the department. We only need an institution here.

from scopus.scopus_author import ScopusAuthor

coauthors = [ScopusAuthor(auid) for auid, name in data]

print(', '.join(['{0} ({1})'.format(au.name, au.current_affiliation.split(',')[0])
                 for au in coauthors
                 if au.current_affiliation.split(',')[0] != 'Carnegie Mellon University']))

Sneha A. Akhade (Pennsylvania State University), Erik J. Albenze (National Energy Technology Laboratory), Federico Calle-Vallejo (Leiden Institute of Chemistry), Robin Chao (National Energy Technology Laboratory), Krishnan V. Damodaran (University of Pittsburgh), Carmeline J. Dsilva (Princeton University), Adefemi A. Egbebi (URS), John C. Eslick (National Energy Technology Laboratory), Anatoly I. Frenkel (Yeshiva University), Kirk R. Gerdes (National Energy Technology Laboratory), Heine Anton Hansen (Danmarks Tekniske Universitet), David P. Hopkinson (National Energy Technology Laboratory), Thomas Francisco Jaramillo (Fermi National Accelerator Laboratory), Yogesh V. Joshi (Exxon Mobil Research and Engineering), Christopher J. Keturakis (Lehigh University), Marc T M Koper (Leiden Institute of Chemistry), Victor A. Kusuma (National Energy Technology Laboratory), James Landon (University of Kentucky), David R. Luebke (Liquid Ion Solutions), Isabelacostinela Man (Universitatea din Bucuresti), James X. Mao (University of Pittsburgh), José Ignacio Martínez (CSIC - Instituto de Ciencia de Materiales de Madrid (ICMM)), David C M Miller (National Energy Technology Laboratory), Bryan D. Morreale (National Energy Technology Laboratory), Christina R. Myers (National Energy Technology Laboratory), Jens Kehlet Nørskov (Stanford Linear Accelerator Center), Rumyana V. Petrova (International Iberian Nanotechnology Laboratory), Vladimir V. Pushkarev (Dow Corning Corporation), Sumathy Raman (Exxon Mobil Research and Engineering), Kevin P. Resnik (URS), Walter Richard Alesi (National Energy Technology Laboratory), Jan Rossmeisl (Kobenhavns Universitet), Edward M. Sabolsky (West Virginia University), Wei Shi (University of Pittsburgh), Nicholas S. Siefert (National Energy Technology Laboratory), Haiyan Su (Dalian Institute of Chemical Physics Chinese Academy of Sciences), Robert Lee Thompson (University of Pittsburgh Medical Center), Relja Vasić (SUNY College of Nanoscale Science and Engineering), Israel E. Wachs (Lehigh University), John D. Watkins (National Energy Technology Laboratory), Chunrong Yin (United States Department of Energy), Xu Zhou (Liquid Ion Solutions)

This is pretty sweet. I could pretty easily create a query that had all the PIs on a proposal, and alphabetize everyone's coauthors, or print them to a CSV file for import to Excel, or whatever format is required for conflict of interest reporting. The list is not perfect, but it is easy to manually fix it here.

That little bit of code is wrapped in a command-line utility in the scopus Python package. You use it like this. Just run it every time you need an updated list of coauthors! It isn't super flexible for now, e.g. excluding multiple affiliations, including multiple authors, etc… isn't fully supported.

./scopus_coauthors 7004212771 2010 --exclude-affiliation="Carnegie Mellon University"

Sneha A. Akhade (Pennsylvania State University), Erik J. Albenze (National Energy Technology Laboratory), Federico Calle-Vallejo (Leiden Institute of Chemistry), Robin Chao (National Energy Technology Laboratory), Krishnan V. Damodaran (University of Pittsburgh), Carmeline J. Dsilva (Princeton University), Adefemi A. Egbebi (URS), John C. Eslick (National Energy Technology Laboratory), Anatoly I. Frenkel (Yeshiva University), Kirk R. Gerdes (National Energy Technology Laboratory), Heine Anton Hansen (Danmarks Tekniske Universitet), David P. Hopkinson (National Energy Technology Laboratory), Thomas Francisco Jaramillo (Fermi National Accelerator Laboratory), Yogesh V. Joshi (Exxon Mobil Research and Engineering), Christopher J. Keturakis (Lehigh University), Marc T M Koper (Leiden Institute of Chemistry), Victor A. Kusuma (National Energy Technology Laboratory), James Landon (University of Kentucky), David R. Luebke (Liquid Ion Solutions), Isabelacostinela Man (Universitatea din Bucuresti), James X. Mao (University of Pittsburgh), José Ignacio Martínez (CSIC - Instituto de Ciencia de Materiales de Madrid (ICMM)), David C M Miller (National Energy Technology Laboratory), Bryan D. Morreale (National Energy Technology Laboratory), Christina R. Myers (National Energy Technology Laboratory), Jens Kehlet Nørskov (Stanford Linear Accelerator Center), Rumyana V. Petrova (International Iberian Nanotechnology Laboratory), Vladimir V. Pushkarev (Dow Corning Corporation), Sumathy Raman (Exxon Mobil Research and Engineering), Kevin P. Resnik (URS), Walter Richard Alesi (National Energy Technology Laboratory), Jan Rossmeisl (Kobenhavns Universitet), Edward M. Sabolsky (West Virginia University), Wei Shi (University of Pittsburgh), Nicholas S. Siefert (National Energy Technology Laboratory), Haiyan Su (Dalian Institute of Chemical Physics Chinese Academy of Sciences), Robert Lee Thompson (University of Pittsburgh Medical Center), Relja Vasić (SUNY College of Nanoscale Science and Engineering), Israel E. Wachs (Lehigh University), John D. Watkins (National Energy Technology Laboratory), Chunrong Yin (United States Department of Energy), Xu Zhou (Liquid Ion Solutions)

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Using the Scopus api with xml output

Posted April 06, 2015 at 09:35 AM | categories: scopus, python, xml | tags:

According to http://api.elsevier.com/documentation/AbstractRetrievalAPI.wadl , the native form of the Scopus abstract document is xml, and the full abstract cannot always be represented as json. So… I am going to just bite the bullet and learn to deal with the xml. This is a companion post to http://kitchingroup.cheme.cmu.edu/blog/2015/04/04/Making-highly-linked-bibliographies-from-the-Scopus-API/ . Most of the code in this post gets tangled out to scopus_xml.py. I know it is not totally robust yet, but I have been using it for a lot of analysis, and it works pretty well so far.

This is another long post, with code that probably runs off screen. You can see the end result of what we do in this post here: http://kitchingroup.cheme.cmu.edu/publications.html .

We start with a general function to return an xml elementtree. We build in some caching to avoid downloading things we already have; this is slow, and there are limits on how many times you can download.

import requests
import os
import xml.etree.ElementTree as ET

from my_scopus import MY_API_KEY

def get_abstract_info(EID, refresh=False):
    'Get and save the json data for EID.'
    base = 'scopus-xml/get_abstract_info'
    if not os.path.exists(base):
        os.makedirs(base)

    fname = '{0}/{1}'.format(base, EID)
    if os.path.exists(fname) and not refresh:
        with open(fname) as f:
            return ET.fromstring(f.read())

    # Otherwise retrieve and save results
    url = ("http://api.elsevier.com/content/abstract/eid/" + EID + '?view=META_ABS')
    resp = requests.get(url,
                    headers={'Accept':'application/xml',
                             'X-ELS-APIKey': MY_API_KEY})
    with open(fname, 'w') as f:
        f.write(resp.text.encode('utf-8'))

    results = ET.fromstring(resp.text.encode('utf-8'))

    return results

Next, we do some introspection to see what we have.

from scopus_xml import *
#results = get_abstract_info('2-s2.0-84896759135')
#results = get_abstract_info('2-s2.0-84924911828')
results = get_abstract_info('2-s2.0-84901638552')
for el in results:
    print el.tag
    for el1 in el:
        print '  -->',el1.tag
    print

{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata --> {http://prismstandard.org/namespaces/basic/2.0/}url --> {http://purl.org/dc/elements/1.1/}identifier --> {http://www.elsevier.com/xml/svapi/abstract/dtd}eid --> {http://prismstandard.org/namespaces/basic/2.0/}doi --> {http://purl.org/dc/elements/1.1/}title --> {http://prismstandard.org/namespaces/basic/2.0/}aggregationType --> {http://www.elsevier.com/xml/svapi/abstract/dtd}srctype --> {http://www.elsevier.com/xml/svapi/abstract/dtd}citedby-count --> {http://prismstandard.org/namespaces/basic/2.0/}publicationName --> {http://purl.org/dc/elements/1.1/}publisher --> {http://www.elsevier.com/xml/svapi/abstract/dtd}source-id --> {http://prismstandard.org/namespaces/basic/2.0/}issn --> {http://prismstandard.org/namespaces/basic/2.0/}volume --> {http://prismstandard.org/namespaces/basic/2.0/}startingPage --> {http://prismstandard.org/namespaces/basic/2.0/}endingPage --> {http://prismstandard.org/namespaces/basic/2.0/}pageRange --> {http://prismstandard.org/namespaces/basic/2.0/}coverDate --> {http://purl.org/dc/elements/1.1/}creator --> {http://purl.org/dc/elements/1.1/}description --> {http://www.elsevier.com/xml/svapi/abstract/dtd}link --> {http://www.elsevier.com/xml/svapi/abstract/dtd}link --> {http://www.elsevier.com/xml/svapi/abstract/dtd}link {http://www.elsevier.com/xml/svapi/abstract/dtd}affiliation --> {http://www.elsevier.com/xml/svapi/abstract/dtd}affilname {http://www.elsevier.com/xml/svapi/abstract/dtd}authors --> {http://www.elsevier.com/xml/svapi/abstract/dtd}author --> {http://www.elsevier.com/xml/svapi/abstract/dtd}author

Now, some examples for myself to see how to get things.

from scopus_xml import *

results = get_abstract_info('2-s2.0-84901638552')

coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')

print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}srctype').text
print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}source-id').text

#authors = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors')
#for author in results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors'):
#    print author.find('{http://www.elsevier.com/xml/ani/common}indexed-name').text

for creator in coredata.find('{http://purl.org/dc/elements/1.1/}creator'):
    print creator.attrib

print coredata.find('{http://purl.org/dc/elements/1.1/}title').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}publicationName').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}coverDate').text
print coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}citedby-count').text
print coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi').text

for link in coredata.findall('{http://www.elsevier.com/xml/svapi/abstract/dtd}link'):
    if link.attrib['rel'] == 'scopus':
        print link.attrib['href']
    else:
        print link.attrib['href']

# alternative xpath to get the link
print coredata.find("./{http://www.elsevier.com/xml/svapi/abstract/dtd}link/[@rel='scopus']").attrib['href']

j 22746 {'auid': '55569461200', 'seq': '1'} Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces Catalysis Communications 52 60-64 2014-07-05 2 10.1016/j.catcom.2013.10.028 http://api.elsevier.com/content/abstract/scopus_id/84901638552 http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84901638552&origin=inward http://api.elsevier.com/content/search/scopus?query=refeid%282-s2.0-84901638552%29 http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84901638552&origin=inward

That is basically it. In the next sections, we basically recreate the previous functions from scopus.py using the xml data.

1 Authors

def get_author_link(EID):
    results = get_abstract_info(EID)
    authors = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}authors')
    if authors is None:
        return 'No authors found'
    s = []

    for author in authors:
        name = author.find('{http://www.elsevier.com/xml/ani/common}indexed-name').text
        auid = author.attrib['auid']
        s += ['<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId={0}">{1}</a>'.format(auid, name)]

    return ', '.join(s)

from scopus_xml import *
print get_author_link('2-s2.0-84896759135')
print get_author_link('2-s2.0-84901638552')

<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=8724572500">Thompson R.L.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=22981503200">Shi W.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=6506329719">Albenze E.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=23004637900">Kusuma V.A.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=55676869000">Hopkinson D.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7003584159">Damodaran K.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=55005205100">Lee A.S.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7004212771">Kitchin J.R.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=6701399651">Luebke D.R.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=24081524800">Nulwala H.</a>
<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=55569461200">Xu Z.</a>, <a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7004212771">Kitchin J.R.</a>

2 Journal

def get_journal_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')

    journal = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}publicationName').text
    sid = coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}source-id').text
    s = '<a href="http://www.scopus.com/source/sourceInfo.url?sourceId={sid}">{journal}</a>'

    return s.format(sid=sid, journal=journal)

from scopus_xml import *
print get_journal_link('2-s2.0-84901638552')

<a href="http://www.scopus.com/source/sourceInfo.url?sourceId=22746">Catalysis Communications</a>

3 DOI link

def get_doi_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    doi = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi')
    if doi is not None: doi = doi.text
    s = '<a href="https://doi.org/{doi}">doi:{doi}</a>'
    return s.format(doi=doi)

from scopus_xml import *
print get_doi_link('2-s2.0-84901638552')

doi:10.1016/j.catcom.2013.10.028

4 Abstract link

def get_abstract_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')

    data = get_abstract_info(EID)

    title = coredata.find('{http://purl.org/dc/elements/1.1/}title').text.encode('utf-8')
    link = coredata.find("./{http://www.elsevier.com/xml/svapi/abstract/dtd}link/[@rel='scopus']").attrib['href'].encode('utf-8')
    s = '<a href="{link}">{title}</a>'
    return s.format(link=link, title=title)

from scopus_xml import *
print get_abstract_link('2-s2.0-84901638552')

Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces

5 Citation image

def get_cite_img_link(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    doi = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}doi')
    if doi is not None: doi = doi.text
    s = '<img src="http://api.elsevier.com/content/abstract/citation-count?doi={doi}&httpAccept=image/jpeg&apiKey={apikey}"></img>'

    return s.format(doi=doi, apikey=MY_API_KEY, cite_link=None)

from scopus_xml import *
print get_cite_img_link('2-s2.0-84901638552')

6 Getting it all together

def get_html_citation(EID):
    results = get_abstract_info(EID)
    coredata = results.find('./{http://www.elsevier.com/xml/svapi/abstract/dtd}coredata')
    s = '{authors}, <i>{title}</i>, {journal}, <b>{volume}{issue}</b>, {pages}, ({year}), {doi}, {cites}.'

    issue = ''
    if coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}issueIdentifier') is not None:
        issue = '({})'.format(    coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}issueIdentifier').text)

    volume = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume')
    if volume is not None:
        volume = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}volume').text
    else:
        volume = 'None'

    pages = ''
    if coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange') is not None:
        pages = 'p. ' + coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}pageRange').text
    elif coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}article-number') is not None:
        pages = coredata.find('{http://www.elsevier.com/xml/svapi/abstract/dtd}article-number').text
    else:
        pages = 'no pages found'


    year = coredata.find('{http://prismstandard.org/namespaces/basic/2.0/}coverDate').text

    return s.format(authors=get_author_link(EID),
                    title=get_abstract_link(EID),
                    journal=get_journal_link(EID),
                    volume=volume,
                    issue=issue,
                    pages=pages,
                    year=year,
                    doi=get_doi_link(EID),
                    cites=get_cite_img_link(EID))

from scopus_xml import *
print '<ol>'
print '<li>',get_html_citation('2-s2.0-84896759135'),'</li>'
print
print '<li>',get_html_citation('2-s2.0-84924911828'),'</li>'
print
print '<li>',get_html_citation('2-s2.0-84901638552'),'</li>'
print '</ol>'

Thompson R.L., Shi W., Albenze E., Kusuma V.A., Hopkinson D., Damodaran K., Lee A.S., Kitchin J.R., Luebke D.R., Nulwala H., Probing the effect of electron donation on CO2 absorbing 1,2,3-triazolide ionic liquids, RSC Advances, 4(25), p. 12748-12755, (2014-03-17), doi:10.1039/c3ra47097k, .
Xu Z., Kitchin J.R., Relationships between the surface electronic and chemical properties of doped 4d and 5d late transition metal dioxides, Journal of Chemical Physics, 142(10), 104703, (2015-03-14), doi:10.1063/1.4914093, .
Xu Z., Kitchin J.R., Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces, Catalysis Communications, 52, p. 60-64, (2014-07-05), doi:10.1016/j.catcom.2013.10.028, .

7 Finally getting my documents

Here we get the EIDs from a search query. We use these in the next section to get a new bibliography.

import requests
import json
from my_scopus import MY_API_KEY
resp = requests.get("http://api.elsevier.com/content/search/scopus?query=AU-ID(7004212771)&field=eid,aggregationType&count=100",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

results = resp.json()

return [[str(r['eid']), str(r['prism:aggregationType'])] for r in results['search-results']["entry"] if str(r['prism:aggregationType']) == 'Journal']

2-s2.0-84924911828	Journal
2-s2.0-84923164062	Journal
2-s2.0-84924778427	Journal
2-s2.0-84924130725	Journal
2-s2.0-84901638552	Journal
2-s2.0-84898934670	Journal
2-s2.0-84896759135	Journal
2-s2.0-84896380535	Journal
2-s2.0-84896585411	Journal
2-s2.0-84916613197	Journal
2-s2.0-84908637059	Journal
2-s2.0-84880986072	Journal
2-s2.0-84881394200	Journal
2-s2.0-84873706643	Journal
2-s2.0-84876703352	Journal
2-s2.0-84867809683	Journal
2-s2.0-84864914806	Journal
2-s2.0-84865730756	Journal
2-s2.0-84864592302	Journal
2-s2.0-84863684845	Journal
2-s2.0-84866142469	Journal
2-s2.0-84861127526	Journal
2-s2.0-80052944171	Journal
2-s2.0-80051809046	Journal
2-s2.0-79953651013	Journal
2-s2.0-79952860396	Journal
2-s2.0-77956568341	Journal
2-s2.0-77954747189	Journal
2-s2.0-77956693843	Journal
2-s2.0-77949916234	Journal
2-s2.0-77955464573	Journal
2-s2.0-72049114200	Journal
2-s2.0-73149124752	Journal
2-s2.0-73149109096	Journal
2-s2.0-67449106405	Journal
2-s2.0-63649114440	Journal
2-s2.0-60849113132	Journal
2-s2.0-58649114498	Journal
2-s2.0-40949100780	Journal
2-s2.0-33750804660	Journal
2-s2.0-20544467859	Journal
2-s2.0-15744396507	Journal
2-s2.0-9744261716	Journal
2-s2.0-13444307808	Journal
2-s2.0-3042820285	Journal
2-s2.0-2942640180	Journal
2-s2.0-0142023762	Journal
2-s2.0-0141924604	Journal
2-s2.0-0037368024	Journal
2-s2.0-0037197884	Journal

8 And my html bibliography

This generates my blog bibliography page..

from scopus_xml import *

import requests
import json
from my_scopus import MY_API_KEY
resp = requests.get("http://api.elsevier.com/content/search/scopus?query=AU-ID(7004212771)&field=eid,aggregationType&count=100",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

results = resp.json()

data = [[str(r['eid']), str(r['prism:aggregationType'])] for r in
        results['search-results']["entry"] if str(r['prism:aggregationType']) == 'Journal']


with open('../publications.html.mako', 'w') as f:
    f.write('''<%inherit file="_templates/site.mako" />
<article class="page_box">
<%self:filter chain="markdown">

<h1>Online collections of our work</h1>
Pick your favorite:
<ul>
<li><a href="http://orcid.org/0000-0003-2625-9232">orcid:0000-0003-2625-9232</a></li>

<li><a href="http://www.researcherid.com/rid/A-2363-2010">researcherid:A-2363-2010</a></li>

<li><a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7004212771">scopusid:7004212771</a></li>

<li><a href="https://scholar.google.com/citations?user=jD_4h7sAAAAJ">Google Scholar</a></li>

<li><a href="https://www.researchgate.net/profile/John_Kitchin">Research Gate</a></li>

<li><a href="https://www.growkudos.com/profiles/40205">Kudos</a></li>
</ul>

<h1>Publications</h1>
The authors are linked to their Scopus page, the title linked to the Scopus abstract, the journal linked to the Scopus journal page, and the DOI is linked to https://doi.org which normally redirects you to the journal page.

<ol reversed="reversed">
''')

    for eid,type in data:
        f.write('<li>{}</li>'.format(get_html_citation(eid)))
    f.write('''</ol>

</%self:filter>
</article>
''')

9 Summary

The XML format is not that intuitive to me. It takes some practice writing robust code, e.g. sometimes the find command does not find anything, and then there is not text attribute to get, so you should check for success on finding things. Also, some text is unicode, and you have to take care to encode it, which my library does not do uniformly. Finally, not all journals have things like volume or issue. My formatting code is not super flexible, so these bibliography entries show None in them occasionally. Still, it is not too bad, and this enables a lot of analysis of your publications, as well as displaying them in different ways. See the result of this page here: http://kitchingroup.cheme.cmu.edu/publications.html

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Making highly linked bibliographies from the Scopus API

Posted April 04, 2015 at 11:32 AM | categories: scopus, python | tags:

A given article entry in a bibliography might have the following kinds of links in it. I think we can generate these from a Scopus query.

We are going to look at the document above, with eid=2-s2.0-84901638552. This is another long post, so here is a teaser of what we are doing. For this eid, we want to generate an html entry where each part of the entry is clickable. Here is what we will be able to do by the end of this post:

from scopus import *

print '<ol>', get_html('2-s2.0-84901638552'), '</ol>'

Xu Z.,Kitchin J.R., Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces, Catalysis Communications, 52, p. 60-64, (2014-07-05), doi:10.1016/j.catcom.2013.10.028, .

In this post, we work out code that works for this document. This code in the form shown here might not work on all entries, e.g. for ones that are in press and are missing data, or for APS journals that have no page range. Later, I will fix those so this is more robust. To minimize repeating the code below, I create a python module here called scopus.py . Tangle it out with org-babel-tangle. As in the last post , I am not sharing my API key here, since it is not clear if that key is private or not.

I like json, so we use that data format here. XML would be more robust, as the Scopus site admits not all of the data can be turned into the json format, but for now we stick to json for its simplicity.

import requests
import json, os
from my_scopus import MY_API_KEY

def get_abstract_info(EID, refresh=False):
    'Get and save the json data for EID.'
    base = 'scopus-data/get_abstract_info'
    if not os.path.exists(base):
        os.makedirs(base)

    fname = '{0}/{1}'.format(base, EID)
    if os.path.exists(fname) and not refresh:
        with open(fname) as f:
            return json.loads(f.read())

    # Otherwise retrieve and save results
    url = ("http://api.elsevier.com/content/abstract/eid/" + EID)
    resp = requests.get(url,
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})
    results = json.loads(resp.text.encode('utf-8'))
    with open(fname, 'w') as f:
        f.write(json.dumps(results))

    return results

1 Author pages

Here, we generate the html that will make each author a clickable link that goes to their Scopus ID author page.

def get_author_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    html = '<a href="http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId={0}">{1}</a>'
    authors = [html.format(auid, name) for auid, name in
               zip([x['@auid'] for x in result['authors']['author']],
                   [x['ce:indexed-name'] for x in result['authors']['author']])]

    return ','.join(authors)

from scopus import *
print get_author_link('2-s2.0-84901638552')

Xu Z.,Kitchin J.R.

2 Journal link

The most important pieces of information we need is the journal name and the source-id from the coredata.

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']
print result['coredata']['source-id']
print result['coredata']['prism:publicationName']

22746
Catalysis Communications

def get_journal_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    sid = result['coredata']['source-id']
    journal = result['coredata']['prism:publicationName']
    s = '<a href="http://www.scopus.com/source/sourceInfo.url?sourceId={sid}">{journal}</a>'

    return s.format(sid=sid, journal=journal)

from scopus import *
print get_journal_link('2-s2.0-84901638552')

Catalysis Communications

3 DOI link

It would be helpful to have a doi link, which is actually independent of Scopus so people without Scopus access can still access information.

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']
print result['coredata']['prism:doi']

10.1016/j.catcom.2013.10.028

def get_doi_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    s = '<a href="https://doi.org/{doi}">doi:{doi}</a>'
    return s.format(doi=result['coredata']['prism:doi'])

from scopus import *
print get_doi_link('2-s2.0-84901638552')

doi:10.1016/j.catcom.2013.10.028

4 Citation count image

It is nice to show impact of a paper by showing the citations. These change with time, so a static view is not ideal. Scopus provides a way to get an image they generate that should update when viewed. We need the doi to get that.

def get_cite_img_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    s = '<img src="http://api.elsevier.com/content/abstract/citation-count?doi={doi}&httpAccept=image/jpeg&apiKey={apikey}"></img>'
    return s.format(doi=result['coredata']['prism:doi'].strip(), apikey=MY_API_KEY)

from scopus import *
print get_cite_img_link('2-s2.0-84901638552')

5 The document link

The document link is sort of buried in the coredata. It seems like & has been replaced by & in the json data so we have to do a clunky fix here.

from scopus import *
EID = '2-s2.0-84901638552'
data = get_abstract_info(EID)
result = data['abstracts-retrieval-response']

print result['coredata']['dc:title']
for ref in result['coredata']['link']:
    if ref['@rel'] == 'scopus':
        print ref['@href'].replace('&amp;', '&')
        break

Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=84901638552&origin=inward

def get_abstract_link(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']
    title = result['coredata']['dc:title']
    for ref in result['coredata']['link']:
        if ref['@rel'] == 'scopus':
            link = ref['@href'].replace('&amp;', '&')

    s = '<a href="{link}">{title}</a>'
    return s.format(link=link, title=title)

from scopus import *
print get_abstract_link('2-s2.0-84901638552')

Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces

6 Putting it all together

Our goal is ultimately an html formatted citation where nearly every piece is a hyperlink to additional information, e.g. each author is linked to their page, the title is linked to the scopus document page, the journal is linked to the scopus journal page, a DOI link, and an image of the number of citations. Here it is.

def get_html(EID):
    data = get_abstract_info(EID)
    result = data['abstracts-retrieval-response']

    s = '<li>{authors}, <i>{title}</i>, {journal}, <b>{volume}{issue}</b>, p. {pages}, ({year}), {doi}, {cites}.</li>'

    issue = ''
    if result['coredata'].get('prism:issue'):
        issue = '({})'.format(result['coredata'].get('prism:issue'))
    return s.format(authors=get_author_link(EID),
                    title=get_abstract_link(EID),
                    journal=get_journal_link(EID),
                    volume=result['coredata'].get('prism:volume'),
                    issue=issue,
                    pages=result['coredata'].get('prism:pageRange'),
                    year=result['coredata'].get('prism:coverDate'),
                    doi=get_doi_link(EID),
                    cites=get_cite_img_link(EID))

from scopus import *
print get_html('2-s2.0-84901638552')

Xu Z.,Kitchin J.R., Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces, Catalysis Communications, 52, p. 60-64, (2014-07-05), doi:10.1016/j.catcom.2013.10.028,

Well, that is the end for now. We have a reusable function that generates a nice HTML formatted citation that links out to many different resources. Why aren't all citations on the web this helpful?

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Getting data from the Scopus API

Posted April 03, 2015 at 03:17 PM | categories: scopus, python | tags:

Updated April 03, 2015 at 03:19 PM

I have been exploring the Scopus API (http://dev.elsevier.com/index.html ) lately. This is a RESTful API that allows you to retrieve data about publications via http requests, i.e. from a script. This service is not free; you need to be at an institution that has a Scopus license.

Scopus is very good at finding your papers, and associating them with a Scopus ID. You don't have to do anything to get one, they make it. I have a Scopus ID (http://www.scopus.com/authid/detail.url?origin=AuthorProfile&authorId=7004212771 ) that has all this data via the web, but I wanted to get this data in a tabular form I could use and analyze. Sure you can download a CSV file from that page and analyze that, but I want to script it. I am just like that ;) To use the API, you need to get an API key (http://www.developers.elsevier.com/action/devprojects ). I still cannot figure out if this key is "private" so I am not going to share mine here. I have stored it in a python file called my_scopus.py, and I will import it in these examples.

The code below is "wide", so apologies in advance that some of it will run out of the usual area it belongs.

1 About me from Scopus

There is an author API that provides a metrics view of a Scopus ID. Here this shows there are about 77 documents for me, cited about 3028 times. Why do I say "about"? Apparently there are two different databases that Scopus uses, one for the web, and one for this API, and they do not return the same data. It is close, but not the same. The API database includes thing that are published after 1995, and it may not be updated as quickly as the web database. For example the web page reports 79 documents and 3143 citations. In the next sections we will use the search API, which returns the same information as what is on the web. Here we just illustrate how to setup an http request in Python. I like json output, so we ask for it.

import requests
import json
from my_scopus import MY_API_KEY

resp = requests.get("http://api.elsevier.com/content/author?author_id=7004212771&view=metrics",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

print json.dumps(resp.json(),
                 sort_keys=True,
                 indent=4, separators=(',', ': '))

{
    "author-retrieval-response": [
        {
            "@_fa": "true",
            "@status": "found",
            "coauthor-count": "90",
            "coredata": {
                "citation-count": "3028",
                "cited-by-count": "2369",
                "dc:identifier": "AUTHOR_ID:7004212771",
                "document-count": "77",
                "prism:url": "http://api.elsevier.com/content/author/author_id/7004212771"
            },
            "h-index": "18"
        }
    ]
}

2 Get my documents from Scopus

To find my documents, we will use the Search API, http://api.elsevier.com/documentation/SCOPUSSearchAPI.wadl . We specify a Scopus ID, and to limit the quantity of data that comes back we specify that we want the dc:identifier field, which corresponds to the scopus id for each document. We will use that in the next section to get info for each document.

import requests
import json
from my_scopus import MY_API_KEY
resp = requests.get("http://api.elsevier.com/content/search/scopus?query=AU-ID(7004212771)&field=dc:identifier&count=100",
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

results = resp.json()

return [[str(r['dc:identifier'])] for r in results['search-results']["entry"]]

SCOPUS_ID:84924911828

SCOPUS_ID:84923164062

SCOPUS_ID:84924778427

SCOPUS_ID:84924130725

SCOPUS_ID:84901638552

SCOPUS_ID:84898934670

SCOPUS_ID:84896759135

SCOPUS_ID:84896380535

SCOPUS_ID:84896585411

SCOPUS_ID:84916613197

SCOPUS_ID:84908637059

SCOPUS_ID:84880986072

SCOPUS_ID:84881394200

SCOPUS_ID:84873706643

SCOPUS_ID:84876703352

SCOPUS_ID:84872843990

SCOPUS_ID:84872872509

SCOPUS_ID:84872845400

SCOPUS_ID:84872841108

SCOPUS_ID:84872855250

SCOPUS_ID:84872864754

SCOPUS_ID:84886483703

SCOPUS_ID:84872854676

SCOPUS_ID:84867809683

SCOPUS_ID:84864914806

SCOPUS_ID:84865730756

SCOPUS_ID:84864592302

SCOPUS_ID:84863684845

SCOPUS_ID:84866142469

SCOPUS_ID:84861127526

SCOPUS_ID:84857224144

SCOPUS_ID:84857197729

SCOPUS_ID:84856818654

SCOPUS_ID:80052944171

SCOPUS_ID:80051860134

SCOPUS_ID:80051809046

SCOPUS_ID:79953651013

SCOPUS_ID:79952860396

SCOPUS_ID:79951537083

SCOPUS_ID:79251517782

SCOPUS_ID:77956568341

SCOPUS_ID:77954747189

SCOPUS_ID:77956693843

SCOPUS_ID:77949916234

SCOPUS_ID:77955464573

SCOPUS_ID:72049114200

SCOPUS_ID:78649528829

SCOPUS_ID:78649504144

SCOPUS_ID:77952266872

SCOPUS_ID:73149124752

SCOPUS_ID:73149109096

SCOPUS_ID:67449106405

SCOPUS_ID:63649114440

SCOPUS_ID:60849113132

SCOPUS_ID:58649114498

SCOPUS_ID:79952218110

SCOPUS_ID:79952292116

SCOPUS_ID:78049295221

SCOPUS_ID:79952296916

SCOPUS_ID:79952225819

SCOPUS_ID:78049231913

SCOPUS_ID:79952234104

SCOPUS_ID:79952301915

SCOPUS_ID:45149129361

SCOPUS_ID:40949100780

SCOPUS_ID:37349101648

SCOPUS_ID:58049109348

SCOPUS_ID:33750804660

SCOPUS_ID:33645645065

SCOPUS_ID:20544467859

SCOPUS_ID:15744396507

SCOPUS_ID:9744261716

SCOPUS_ID:13444307808

SCOPUS_ID:3042820285

SCOPUS_ID:2942640180

SCOPUS_ID:0142023762

SCOPUS_ID:0141924604

SCOPUS_ID:0037368024

SCOPUS_ID:0037197884

3 Retrieve info for a document

Here, we work out how to retrieve data for a document. We use the Abstract API (http://api.elsevier.com/documentation/AbstractRetrievalAPI.wadl ). We again use a field to limit the amount of data. Here is an example that works for an article. Scopus also lists books and conferences so, we will see how that works later. Note the unicode stuff. I was getting some errors about non-ascii characters causing the json file not to read, and then issues in constructing the string. This was only a problem for some entries.

import requests
import json
from my_scopus import MY_API_KEY

def get_scopus_info(SCOPUS_ID):
    url = ("http://api.elsevier.com/content/abstract/scopus_id/"
          + SCOPUS_ID
          + "?field=authors,title,publicationName,volume,issueIdentifier,"
          + "prism:pageRange,coverDate,article-number,doi,citedby-count,prism:aggregationType")
    resp = requests.get(url,
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})
    results = json.loads(resp.text.encode('utf-8'))

    fstring = '{authors}, {title}, {journal}, {volume}, {articlenum}, ({date}). {doi} (cited {cites} times).\n'
    return fstring.format(authors=', '.join([au['ce:indexed-name'] for au in results['abstracts-retrieval-response']['authors']['author']]),
                          title=results['abstracts-retrieval-response']['coredata']['dc:title'].encode('utf-8'),
                          journal=results['abstracts-retrieval-response']['coredata']['prism:publicationName'].encode('utf-8'),
                          volume=results['abstracts-retrieval-response']['coredata']['prism:volume'].encode('utf-8'),
                          articlenum=(results['abstracts-retrieval-response']['coredata'].get('prism:pageRange') or
                              results['abstracts-retrieval-response']['coredata'].get('article-number')).encode('utf-8'),
                          date=results['abstracts-retrieval-response']['coredata']['prism:coverDate'].encode('utf-8'),
                          doi='doi:' + results['abstracts-retrieval-response']['coredata']['prism:doi'].encode('utf-8'),
                          cites=int(results['abstracts-retrieval-response']['coredata']['citedby-count'].encode('utf-8')))



print get_scopus_info('SCOPUS_ID:0037368024')

Kitchin J.R., Barteau M.A., Chen J.G., A comparison of gold and molybdenum nanoparticles on TiO2(1 1 0) 1 × 2 reconstructed single crystal surfaces, Surface Science, 526, 323-331, (2003-03-01). doi:10.1016/S0039-6028(02)02679-1 (cited 27 times).

4 Get information for all documents

We will use the data we previously got in the long list of Scopus IDs. A few subtle points here are that I made that a nested list so it would print as a column, and so we will have to index each entry to get the scopus id. Also, it seems that some entries generate json that cannot be parsed by python, so we wrap this in a try block and skip those entries. We need to check for the entry being a Journal article, to avoid errors with our format string. We also need to accomodate journals that do not have page ranges, but have artice numbers instead. Finally, we will format each entry so there is some html code for it.

import requests
import json
import textwrap
from my_scopus import MY_API_KEY

def get_scopus_info(SCOPUS_ID):
    url = ("http://api.elsevier.com/content/abstract/scopus_id/"
          + SCOPUS_ID
          + "?field=authors,title,publicationName,volume,issueIdentifier,"
          + "prism:pageRange,coverDate,article-number,doi,citedby-count,prism:aggregationType")
    resp = requests.get(url,
                    headers={'Accept':'application/json',
                             'X-ELS-APIKey': MY_API_KEY})

    return json.loads(resp.text.encode('utf-8'))


i = 0
for sid in scopus_ids:
    # some entries seem to have json parse errors, so we catch those
    try:
        results = get_scopus_info(sid[0])  # index 0 because the input data is a 2d array
        if results['abstracts-retrieval-response']['coredata']['prism:aggregationType'] == 'Journal':
            i += 1
            fstring = '{authors}, {title}, {journal}, {volume}, {articlenum}, ({date}). <a href="https://doi.org/{doi}">{doi}</a> (cited {cites} times)\n\n'

            s = fstring.format(authors=', '.join([au['ce:indexed-name'].encode('utf-8') for au in results['abstracts-retrieval-response']['authors']['author']]),
                               title=results['abstracts-retrieval-response']['coredata']['dc:title'].encode('utf-8'),
                               journal=results['abstracts-retrieval-response']['coredata']['prism:publicationName'].encode('utf-8'),
                               volume=results['abstracts-retrieval-response']['coredata'].get('prism:volume', 'None').encode('utf-8'),
                               articlenum=str((results['abstracts-retrieval-response']['coredata'].get('prism:pageRange') or
                                           results['abstracts-retrieval-response']['coredata'].get('article-number'))).encode('utf-8'),
                               date=results['abstracts-retrieval-response']['coredata']['prism:coverDate'].encode('utf-8'),
                               doi='doi:' + results['abstracts-retrieval-response']['coredata']['prism:doi'].encode('utf-8'),
                               cites=int(results['abstracts-retrieval-response']['coredata']['citedby-count'].encode('utf-8')))
            print '{0:3d}. {1}<br>'.format(i, s)
    except:
        print '{0:3d}. {1}'.format(i, sid)

1. Xu Z., Kitchin J.R., Relationships between the surface electronic and chemical properties of doped 4d and 5d late transition metal dioxides, Journal of Chemical Physics, 142, 104703, (2015-03-14). doi:10.1063/1.4914093 (cited 0 times)
2. Boes J.R., Gumuslu G., Miller J.B., Gellman A.J., Kitchin J.R., Estimating bulk-composition-dependent H2 adsorption energies on CuxPd1- x alloy (111) surfaces, ACS Catalysis, 5, 1020-1026, (2015-02-06). doi:10.1021/cs501585k (cited 0 times)
3. Boes J.R., Kondratyuk P., Yin C., Miller J.B., Gellman A.J., Kitchin J.R., Core level shifts in Cu-Pd alloys as a function of bulk composition and structure, Surface Science, None, None, (2015-01-01). doi:10.1016/j.susc.2015.02.011 (cited 0 times)
4. Xu Z., Rossmeisl J., Kitchin J.R., A linear response DFT+U study of trends in the oxygen evolution activity of transition metal rutile dioxides, Journal of Physical Chemistry C, 119, 4827-4833, (2015-01-01). doi:10.1021/jp511426q (cited 0 times)
5. Xu Z., Kitchin J.R., Relating the electronic structure and reactivity of the 3d transition metal monoxide surfaces, Catalysis Communications, 52, 60-64, (2014-07-05). doi:10.1016/j.catcom.2013.10.028 (cited 2 times)
6. Demeter E.L., Hilburg S.L., Washburn N.R., Collins T.J., Kitchin J.R., Electrocatalytic oxygen evolution with an immobilized TAML activator, Journal of the American Chemical Society, 136, 5603-5606, (2014-04-16). doi:10.1021/ja5015986 (cited 4 times)
7. Thompson R.L., Shi W., Albenze E., Kusuma V.A., Hopkinson D., Damodaran K., Lee A.S., Kitchin J.R., Luebke D.R., Nulwala H., Probing the effect of electron donation on CO2 absorbing 1,2,3-triazolide ionic liquids, RSC Advances, 4, 12748-12755, (2014-03-17). doi:10.1039/c3ra47097k (cited 1 times)
8. Mehta P., Salvador P.A., Kitchin J.R., Identifying potential BO2 oxide polymorphs for epitaxial growth candidates, ACS Applied Materials and Interfaces, 6, 3630-3639, (2014-03-12). doi:10.1021/am4059149 (cited 0 times)
9. Miller S.D., Pushkarev V.V., Gellman A.J., Kitchin J.R., Simulating temperature programmed desorption of oxygen on Pt(111) using DFT derived coverage dependent desorption barriers, Topics in Catalysis, 57, 106-117, (2014-02-01). doi:10.1007/s11244-013-0166-3 (cited 2 times)
10. Curnan M.T., Kitchin J.R., Effects of concentration, crystal structure, magnetism, and electronic structure method on first-principles oxygen vacancy formation energy trends in perovskites, Journal of Physical Chemistry C, 118, 28776-28790, (2014-01-01). doi:10.1021/jp507957n (cited 2 times)
11. Xu Z., Kitchin J.R., Probing the coverage dependence of site and adsorbate configurational correlations on (111) surfaces of late transition metals, Journal of Physical Chemistry C, 118, 25597-25602, (2014-01-01). doi:10.1021/jp508805h (cited 0 times)
12. Lee A.S., Eslick J.C., Miller D.C., Kitchin J.R., Comparisons of amine solvents for post-combustion CO2 capture: A multi-objective analysis approach, International Journal of Greenhouse Gas Control, 18, 68-74, (2013-10-01). doi:10.1016/j.ijggc.2013.06.020 (cited 3 times)
13. Hallenbeck A.P., Kitchin J.R., Effects of O2 and SO2 on the capture capacity of a primary-amine based polymeric CO2 sorbent, Industrial and Engineering Chemistry Research, 52, 10788-10794, (2013-08-07). doi:10.1021/ie400582a (cited 7 times)
13. ['SCOPUS_ID:84873706643'] 14. Calle-Vallejo F., Inoglu N.G., Su H.-Y., Martinez J.I., Man I.C., Koper M.T.M., Kitchin J.R., Rossmeisl J., Number of outer electrons as descriptor for adsorption processes on transition metals and their oxides, Chemical Science, 4, 1245-1249, (2013-03-01). doi:10.1039/c2sc21601a (cited 16 times)
15. Lee A.S., Kitchin J.R., Chemical and molecular descriptors for the reactivity of amines with CO 2 , Industrial and Engineering Chemistry Research, 51, 13609-13618, (2012-10-24). doi:10.1021/ie301419q (cited 3 times)
16. Rubin E.S., Mantripragada H., Marks A., Versteeg P., Kitchin J., The outlook for improved carbon capture technology, Progress in Energy and Combustion Science, 38, 630-671, (2012-10-01). doi:10.1016/j.pecs.2012.03.003 (cited 91 times)
17. Akhade S.A., Kitchin J.R., Effects of strain, d-band filling, and oxidation state on the surface electronic structure and reactivity of 3d perovskite surfaces, Journal of Chemical Physics, 137, 084703, (2012-08-28). doi:10.1063/1.4746117 (cited 8 times)
18. Landon J., Demeter E., Inoglu N., Keturakis C., Wachs I.E., Vasic R., Frenkel A.I., Kitchin J.R., Spectroscopic characterization of mixed Fe-Ni oxide electrocatalysts for the oxygen evolution reaction in alkaline electrolytes, ACS Catalysis, 2, 1793-1801, (2012-08-03). doi:10.1021/cs3002644 (cited 39 times)
19. Chao R., Munprom R., Petrova R., Gerdes K., Kitchin J.R., Salvador P.A., Structure and relative thermal stability of mesoporous (La, Sr) MnO 3powders prepared using evaporation-induced self-assembly methods, Journal of the American Ceramic Society, 95, 2339-2346, (2012-07-01). doi:10.1111/j.1551-2916.2012.05236.x (cited 4 times)
20. Kitchin J., Preface: Trends in computational catalysis, Topics in Catalysis, 55, 227-228, (2012-06-01). doi:10.1007/s11244-012-9808-0 (cited 0 times)
21. Alesi W.R., Kitchin J.R., Evaluation of a primary amine-functionalized ion-exchange resin for CO 2 capture, Industrial and Engineering Chemistry Research, 51, 6907-6915, (2012-05-16). doi:10.1021/ie300452c (cited 15 times)
22. Akhade S.A., Kitchin J.R., Effects of strain, d-band filling, and oxidation state on the bulk electronic structure of cubic 3d perovskites, Journal of Chemical Physics, 135, 104702, (2011-09-14). doi:10.1063/1.3631948 (cited 3 times)
23. Man I.C., Su H.-Y., Calle-Vallejo F., Hansen H.A., Martinez J.I., Inoglu N.G., Kitchin J., Jaramillo T.F., Norskov J.K., Rossmeisl J., Universality in Oxygen Evolution Electrocatalysis on Oxide Surfaces, ChemCatChem, 3, 1159-1165, (2011-07-11). doi:10.1002/cctc.201000397 (cited 199 times)
24. Inoglu N., Kitchin J.R., Identification of sulfur-tolerant bimetallic surfaces using dft parametrized models and atomistic thermodynamics, ACS Catalysis, 1, 399-407, (2011-04-01). doi:10.1021/cs200039t (cited 9 times)
25. Miller S.D., Inoglu N., Kitchin J.R., Configurational correlations in the coverage dependent adsorption energies of oxygen atoms on late transition metal fcc(111) surfaces, Journal of Chemical Physics, 134, 104709, (2011-03-14). doi:10.1063/1.3561287 (cited 16 times)
26. Alesi Jr. W.R., Gray M., Kitchin J.R., CO2 adsorption on supported molecular amidine systems on activated carbon, ChemSusChem, 3, 948-956, (2010-08-01). doi:10.1002/cssc.201000056 (cited 18 times)
27. Landon J., Kitchin J.R., Electrochemical concentration of carbon dioxide from an oxygen/carbon dioxide containing gas stream, Journal of the Electrochemical Society, 157, None, (2010-07-23). doi:10.1149/1.3432440 (cited 3 times)
28. Inoglu N., Kitchin J.R., Simple model explaining and predicting coverage-dependent atomic adsorption energies on transition metal surfaces, Physical Review B - Condensed Matter and Materials Physics, 82, 045414, (2010-07-16). doi:10.1103/PhysRevB.82.045414 (cited 14 times)
29. Pennline H.W., Granite E.J., Luebke D.R., Kitchin J.R., Landon J., Weiland L.M., Separation of CO2 from flue gas using electrochemical cells, Fuel, 89, 1307-1314, (2010-06-01). doi:10.1016/j.fuel.2009.11.036 (cited 20 times)
30. Inoglu N., Kitchin J.R., New solid-state table: Estimating d-band characteristics for transition metal atoms, Molecular Simulation, 36, 633-638, (2010-06-01). doi:10.1080/08927022.2010.481794 (cited 16 times)
31. Tierney H.L., Baber A.E., Kitchin J.R., Sykes E.C.H., Hydrogen dissociation and spillover on individual isolated palladium atoms, Physical Review Letters, 103, 246102, (2009-12-10). doi:10.1103/PhysRevLett.103.246102 (cited 45 times)
32. Miller S.D., Kitchin J.R., Uncertainty and figure selection for DFT based cluster expansions for oxygen adsorption on Au and Pt (111) surfaces, Molecular Simulation, 35, 920-927, (2009-09-01). doi:10.1080/08927020902833137 (cited 14 times)
33. Inolu N., Kitchin J.R., Sulphur poisoning of water-gas shift catalysts: Site blocking and electronic structure modification, Molecular Simulation, 35, 936-941, (2009-09-01). doi:10.1080/08927020902833129 (cited 6 times)
34. Kitchin J.R., Correlations in coverage-dependent atomic adsorption energies on Pd(111), Physical Review B - Condensed Matter and Materials Physics, 79, 205412, (2009-05-01). doi:10.1103/PhysRevB.79.205412 (cited 26 times)
35. Han J.W., Kitchin J.R., Sholl D.S., Step decoration of chiral metal surfaces, Journal of Chemical Physics, 130, 124710, (2009-04-08). doi:10.1063/1.3096964 (cited 11 times)
36. Miller S.D., Kitchin J.R., Relating the coverage dependence of oxygen adsorption on Au and Pt fcc(1 1 1) surfaces through adsorbate-induced surface electronic structure effects, Surface Science, 603, 794-801, (2009-03-01). doi:10.1016/j.susc.2009.01.021 (cited 39 times)
37. Inoglu N., Kitchin J.R., Atomistic thermodynamics study of the adsorption and the effects of water-gas shift reactants on Cu catalysts under reaction conditions, Journal of Catalysis, 261, 188-194, (2009-01-25). doi:10.1016/j.jcat.2008.11.020 (cited 20 times)
38. Kitchin J.R., Reuter K., Scheffler M., Alloy surface segregation in reactive environments: First-principles atomistic thermodynamics study of Ag3 Pd(111) in oxygen atmospheres, Physical Review B - Condensed Matter and Materials Physics, 77, 075437, (2008-02-29). doi:10.1103/PhysRevB.77.075437 (cited 49 times)
39. Norskov J.K., Bligaard T., Logadottir A., Kitchin J.R., Chen J.G., Pandelov S., Stimming U., Response to "comment on 'trends in the exchange current for hydrogen evolution' [J. Electrochem. Soc., 152, J23 (2005)]", Journal of the Electrochemical Society, 153, 054612JES, (2006-11-14). doi:10.1149/1.2358292 (cited 9 times)
40. Kitchin J.R., Norskov J.K., Barteau M.A., Chen J.G., Trends in the chemical properties of early transition metal carbide surfaces: A density functional study, Catalysis Today, 105, 66-73, (2005-07-15). doi:10.1016/j.cattod.2005.04.008 (cited 70 times)
41. Norskov J.K., Bligaard T., Logadottir A., Kitchin J.R., Chen J.G., Pandelov S., Stimming U., Trends in the exchange current for hydrogen evolution, Journal of the Electrochemical Society, 152, None, (2005-04-07). doi:10.1149/1.1856988 (cited 282 times)
42. Norskov J.K., Rossmeisl J., Logadottir A., Lindqvist L., Kitchin J.R., Bligaard T., Jonsson H., Origin of the overpotential for oxygen reduction at a fuel-cell cathode, Journal of Physical Chemistry B, 108, 17886-17892, (2004-11-18). doi:10.1021/jp047349j (cited 1055 times)
43. Kitchin J.R., Norskov J.K., Barteau M.A., Chen J.G., Role of strain and ligand effects in the modification of the electronic and chemical Properties of bimetallic surfaces, Physical Review Letters, 93, None, (2004-10-08). doi:10.1103/PhysRevLett.93.156801 (cited 361 times)
44. Mhadeshwar A.B., Kitchin J.R., Barteau M.A., Vlachos D.G., The role of adsorbate-adsorbate interactions in the rate controlling step and the most abundant reaction intermediate of NH 3 decomposition on RU, Catalysis Letters, 96, 13-22, (2004-07-01). doi:10.1023/B:CATL.0000029523.22277.e1 (cited 45 times)
45. Kitchin J.R., Norskov J.K., Barteau M.A., Chen J.G., Modification of the surface electronic and chemical properties of Pt(111) by subsurface 3d transition metals, Journal of Chemical Physics, 120, 10240-10246, (2004-06-01). doi:10.1063/1.1737365 (cited 443 times)
46. McCormick J.R., Kitchin J.R., Barteau M.A., Chen J.G., A four-point probe correlation of oxygen sensitivity to changes in surface resistivity of TiO2(0 0 1) and Pd-modified TiO2(0 0 1), Surface Science, 545, None, (2003-11-01). doi:10.1016/j.susc.2003.08.041 (cited 11 times)
47. Kitchin J.R., Khan N.A., Barteau M.A., Chen J.G., Yakshinskiy B., Madey T.E., Elucidation of the active surface and origin of the weak metal-hydrogen bond on Ni/Pt(1 1 1) bimetallic surfaces: A surface science and density functional theory study, Surface Science, 544, 295-308, (2003-10-20). doi:10.1016/j.susc.2003.09.007 (cited 108 times)
48. Kitchin J.R., Barteau M.A., Chen J.G., A comparison of gold and molybdenum nanoparticles on TiO2(1 1 0) 1 × 2 reconstructed single crystal surfaces, Surface Science, 526, 323-331, (2003-03-01). doi:10.1016/S0039-6028(02)02679-1 (cited 27 times)
49. Song I.K., Kitchin J.R., Barteau M.A., H3PW12O40-functionalized tip for scanning tunneling microscopy, Proceedings of the National Academy of Sciences of the United States of America, 99, 6471-6475, (2002-04-30). doi:10.1073/pnas.072514399 (cited 12 times)

5 Summary thoughts

I see a lot of potential here for analytics on publications, generation of bibliography files, etc… Instead of retrieving this data every time, it would make much more sense to cache it, e.g. writing each result to a file that could then be used locally, and much faster. The downside of that is, the citations would not be updated in those files. The upside is, you could fix the titles so they are properly marked up. I do not know what the issues with some of the json files was. Some of them were unicode issues. Some other day I will try to track down the other ones.

The entries could be made a lot more functional than this. Each author could be turned into a link back to the scopus author page, for example, the title could be linked to the scopus abstract page, etc… The citations could be a button that automatically updates (like the one in this post ). That is another exercise, for another day!

org-mode source

Org-mode version = 8.2.10

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