9. Research articles vs datasets in chemistry and materials science#
In this notebook, we show how to retrieve meta information about papers and datasets to make a comparison between the number of research articles published in chemistry and materials science (Web of Science Core Collection) and the number of datasets deposited in data repositories (DataCite and ZENODO) from 1996 to 2023.
9.1. Example of data collection using the Web of Science API#
import os
import pandas as pd
import requests
import urllib.parse
import json
import time
import matextract # noqa: F401
9.1.1. Create a function to request data from Web of Science#
def wos_api_request(i, query, wos_data):
request = requests.get(
f"https://api.clarivate.com/apis/wos-starter/v1/documents?db=WOS&q=TS=({urllib.parse.quote(query)})&"
f"&limit=50&page={i+1}",
headers={"X-APIKey": os.environ["WOS_API_KEY"]},
)
try:
for wos_record in request.json()["hits"]:
wos_data.append(wos_record)
except (
requests.exceptions.ConnectionError,
requests.exceptions.JSONDecodeError,
KeyError,
):
print(f"Resending WoS API request #{i+1}")
time.sleep(100)
wos_api_request(i, query, wos_data)
9.1.2. Create a function to get Article and Data Paper document types published between 1996 and 2023#
def process_data(wos_data):
years = []
for paper in wos_data:
if "Article" in paper["types"] or "Data Paper" in paper["types"]:
if 1996 <= int(paper["source"]["publishYear"]) <= 2023:
pub_year = int(paper["source"]["publishYear"])
if len(years) == 0:
years.append(
{
"publication_year": pub_year,
"wos_documents": 1,
}
)
else:
for year in years:
if year["publication_year"] == pub_year:
year["wos_documents"] += 1
break
else:
years.append(
{
"publication_year": pub_year,
"wos_documents": 1,
}
)
return years
9.1.3. Create a function to save the results in a .csv file#
def save_results(file_name, years):
years.sort(reverse=True, key=lambda years: years["wos_documents"])
df = pd.DataFrame(data=years)
column_names = {
"publication_year": "publication_year",
"wos_documents": "wos_documents",
}
df.rename(columns=column_names, inplace=True)
df.to_csv(f"./wos_results/{file_name}.csv", sep=";", index=False)
9.1.4. Example of data collection on “thermoelectric materials”#
As an example, we extract from the Web of Science Core Collection the papers published on thermoelectric materials.
wos_data = []
query = "thermoelectric AND materials"
We send an initial WoS API request to assess the number of requests required to extract all the papers in this topic. From the initial response, we extract the total number of records found.
initial_wos_response = requests.get(
f"https://api.clarivate.com/apis/wos-starter/v1/documents?db=WOS&q=TS=({urllib.parse.quote(query)})&"
f"&limit=50&page=1",
headers={"X-APIKey": os.environ["WOS_API_KEY"]},
)
data = initial_wos_response.json()
print(f"Number of papers from the query ({query}): {data['metadata']['total']}")
Number of papers from the query (thermoelectric AND materials): 29704
With the total number of records, we calculate the number of requests required.
wos_requests_required = ((data["metadata"]["total"] - 1) // 50) + 1
print(f"Number of requests required: {wos_requests_required}")
Number of requests required: 595
Now we can extract the papers from WoS. This can take several minutes, depending on the total number of records to be collected.
for i in range(wos_requests_required + 1):
wos_api_request(i, query, wos_data)
print(
f"{(((i + 1) * 100) / wos_requests_required):.1f}% of WoS API requests complete"
)
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We obtain a list of dictionaries including all the records extracted (as an example, the data for the first paper is shown below). We can save these raw results in a .json file.
wos_data[0]
{'uid': 'WOS:000187876000038',
'title': 'A critical study of the thermoelectric method of measuring vapor pressure',
'types': ['Article'],
'sourceTypes': ['Article'],
'source': {'sourceTitle': 'JOURNAL OF BIOLOGICAL CHEMISTRY',
'publishYear': 1938,
'publishMonth': 'NOV',
'volume': '126',
'issue': '1',
'pages': {'range': '349-360', 'begin': '349', 'end': '360', 'count': 12}},
'names': {'authors': [{'displayName': 'Roepke, RR',
'wosStandard': 'Roepke, RR',
'researcherId': 'FXG-1059-2022'},
{'displayName': 'Baldes, EJ',
'wosStandard': 'Baldes, EJ',
'researcherId': 'EKH-9490-2022'}]},
'links': {'record': 'https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=incarcsic_woslite&SrcAuth=WosAPI&KeyUT=WOS:000187876000038&DestLinkType=FullRecord&DestApp=WOS_CPL',
'citingArticles': 'https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=incarcsic_woslite&SrcAuth=WosAPI&KeyUT=WOS:000187876000038&DestLinkType=CitingArticles&DestApp=WOS_CPL',
'references': 'https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=incarcsic_woslite&SrcAuth=WosAPI&KeyUT=WOS:000187876000038&DestLinkType=CitedReferences&DestApp=WOS',
'related': 'https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=incarcsic_woslite&SrcAuth=WosAPI&KeyUT=WOS:000187876000038&DestLinkType=RelatedRecords&DestApp=WOS_CPL'},
'citations': [{'db': 'WOS', 'count': 10}],
'identifiers': {'eissn': '1083-351X'},
'keywords': {'authorKeywords': []}}
with open("wos_data_output.json", "w") as file:
json.dump(wos_data, file)
with open("wos_data_output.json") as file:
wos_data = json.load(file)
len(wos_data)
29704
We process the obtained data with the function process_data and save the results in a .csv file with the function save_results.
years = process_data(wos_data)
save_results("thermoelectric", years)
papers = 0
for year in years:
papers += year["wos_documents"]
print(
f"Number of papers published between 1996 and 2023 from the query ({query}): {papers}"
)
Number of papers published between 1996 and 2023 from the query (thermoelectric AND materials): 22867
Following this procedure, we have extracted from WoS the data on published papers (Articles and Data Papers) for the main categories of materials studied in chemistry. Using the corresponding APIs, we can also extract the number of datasets published in the DataCite and ZENODO repositories for the same categories.
9.2. Collecting the saved data for all categories from WoS, DataCite and ZENODO#
In this section, we prepare the collected data on papers and datasets to plot the results as a function of the categories and publication years.
from glob import glob
all_results = glob("./wos_results/*.csv")
print(f"files found: {len(all_results)}")
files found: 9
all_results
['./wos_results/nanoparticles.csv',
'./wos_results/polymers.csv',
'./wos_results/mofs.csv',
'./wos_results/photocatalytic.csv',
'./wos_results/biomaterials.csv',
'./wos_results/thermoelectric.csv',
'./wos_results/battery_cathode.csv',
'./wos_results/2Dmaterials.csv',
'./wos_results/semiconductor.csv']
We create a .csv file combining the results of the different categories.
df = pd.read_csv(all_results[0], sep=";")
df.head()
| publication_year | wos_documents | |
|---|---|---|
| 0 | 2023 | 76010 |
| 1 | 2022 | 79936 |
| 2 | 2021 | 73154 |
| 3 | 2020 | 75213 |
| 4 | 2019 | 70984 |
df = df.sort_values(by="publication_year").reset_index(drop=True)
df_results = pd.DataFrame(df["publication_year"].reset_index(drop=True)).copy()
df_results.head()
| publication_year | |
|---|---|
| 0 | 1996 |
| 1 | 1997 |
| 2 | 1998 |
| 3 | 1999 |
| 4 | 2000 |
materials_name = [
"nanoparticles",
"battery_cathode",
"photocatalytic",
"polymers",
"thermoelectric",
"mofs",
"biomaterials",
"2Dmaterials",
"semiconductor",
]
for file in materials_name:
df = pd.read_csv(f"./wos_results/{file}.csv", sep=";")
df = df.sort_values(by="publication_year").reset_index(drop=True)
df = df.rename(columns={"wos_documents": file})
df_results = pd.merge(df_results, df)
df_results.head()
| publication_year | nanoparticles | battery_cathode | photocatalytic | polymers | thermoelectric | mofs | biomaterials | 2Dmaterials | semiconductor | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1996 | 312 | 49 | 15 | 12406 | 142 | 30 | 233 | 121 | 570 |
| 1 | 1997 | 454 | 56 | 18 | 12661 | 146 | 44 | 240 | 137 | 654 |
| 2 | 1998 | 749 | 97 | 25 | 13879 | 212 | 37 | 294 | 164 | 695 |
| 3 | 1999 | 1022 | 121 | 28 | 14713 | 226 | 47 | 347 | 178 | 721 |
| 4 | 2000 | 1298 | 160 | 27 | 15088 | 294 | 45 | 345 | 188 | 666 |
df_results.info()
<class 'pandas.core.frame.DataFrame'>
RangeIndex: 28 entries, 0 to 27
Data columns (total 10 columns):
# Column Non-Null Count Dtype
--- ------ -------------- -----
0 publication_year 28 non-null int64
1 nanoparticles 28 non-null int64
2 battery_cathode 28 non-null int64
3 photocatalytic 28 non-null int64
4 polymers 28 non-null int64
5 thermoelectric 28 non-null int64
6 mofs 28 non-null int64
7 biomaterials 28 non-null int64
8 2Dmaterials 28 non-null int64
9 semiconductor 28 non-null int64
dtypes: int64(10)
memory usage: 2.3 KB
df_results.to_csv("wos_materials_papers.csv", sep=",", index=False)
9.3. Plot the number of research papers vs. datasets deposited in data repositories in chemistry and materials science per year#
9.3.1. Load data on papers from Web of Science#
df_wos = pd.read_csv("wos_materials_papers.csv", sep=",")
df_wos.head()
| publication_year | nanoparticles | battery_cathode | photocatalytic | polymers | thermoelectric | mofs | biomaterials | 2Dmaterials | semiconductor | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1996 | 312 | 49 | 15 | 12406 | 142 | 30 | 233 | 121 | 570 |
| 1 | 1997 | 454 | 56 | 18 | 12661 | 146 | 44 | 240 | 137 | 654 |
| 2 | 1998 | 749 | 97 | 25 | 13879 | 212 | 37 | 294 | 164 | 695 |
| 3 | 1999 | 1022 | 121 | 28 | 14713 | 226 | 47 | 347 | 178 | 721 |
| 4 | 2000 | 1298 | 160 | 27 | 15088 | 294 | 45 | 345 | 188 | 666 |
9.3.2. Load data on DataCite datasets#
df_datacite = pd.read_csv("datacite_datasets.csv", sep=";")
df_datacite.head()
| publication_year | nanoparticles | battery_cathode | photocatalytic | polymers | thermoelectric | mofs | biomaterials | 2Dmaterials | semiconductor | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 2010 | 17 | NaN | NaN | 11 | NaN | 1 | 1 | 2 | NaN |
| 1 | 2011 | 36 | NaN | NaN | 4 | 1.0 | 1 | 2 | 4 | NaN |
| 2 | 2012 | 30 | NaN | NaN | 41 | NaN | 1 | 2 | 4 | NaN |
| 3 | 2013 | 52 | NaN | NaN | 12 | 1.0 | 1 | 2 | 139 | 1.0 |
| 4 | 2014 | 148 | 1.0 | 1.0 | 53 | 1.0 | 3 | 8 | 33 | 1.0 |
9.3.3. Load data on ZENODO datasets#
df_zenodo = pd.read_csv("zenodo_datasets.csv", sep=";")
df_zenodo.head()
| publication_year | nanoparticles | battery_cathode | photocatalytic | polymers | thermoelectric | mofs | biomaterials | 2Dmaterials | semiconductor | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 2010 | NaN | NaN | NaN | NaN | NaN | NaN | 1.0 | NaN | NaN |
| 1 | 2011 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 2 | 2012 | 2.0 | NaN | NaN | 1.0 | NaN | NaN | NaN | NaN | NaN |
| 3 | 2013 | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN |
| 4 | 2014 | NaN | NaN | NaN | 2.0 | NaN | 1.0 | NaN | NaN | NaN |
9.3.4. Unify labels and colors#
labels = [
"nanoparticles",
"battery cathode materials",
"photocatalytic materials",
"polymers",
"thermoelectric materials",
"MOFs",
"biomaterials",
"2D materials",
"semiconductor materials",
]
colors = [
"#1a4a81",
"#2166ac",
"#4393c3",
"#92c5de",
"#c2e1f2",
"#f4a582",
"#d6604d",
"#b2182b",
"#67001f",
]
9.3.5. Plot WoS chemistry and materials science papers vs. year using plotly.express#
import plotly.express as px
fig = px.bar(
data_frame=df_wos,
x="publication_year",
y=df_wos.columns[1:],
barmode="relative",
color_discrete_sequence=colors,
)
for i, trace in enumerate(fig.data):
trace.update(name=labels[i])
fig.update_layout(
{"plot_bgcolor": "#FFFFFF", "paper_bgcolor": "#FFFFFF"},
width=900,
height=500,
margin=dict(l=100, r=40, t=20, b=45),
font_family="Arial",
font_color="#646363",
font_size=20,
title_font_family="Arial",
title_font_color="#646363",
legend_title_text=None,
legend=dict(font={"size": 18}, yanchor="bottom", y=0.44, xanchor="left", x=0.04),
)
fig.update_yaxes(
title_text="no. WoS papers",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 24}},
range=(0, 220000),
tickformat=".2s",
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
)
fig
9.3.6. Plot DataCite datasets papers vs. year using plotly.express#
fig = px.bar(
data_frame=df_datacite,
x="publication_year",
y=df_datacite.columns[1:],
barmode="relative",
color_discrete_sequence=colors,
)
for i, trace in enumerate(fig.data):
trace.update(name=labels[i])
fig.update_layout(
{"plot_bgcolor": "#FFFFFF", "paper_bgcolor": "#FFFFFF"},
width=900,
height=350,
margin=dict(l=90, r=40, t=30, b=45),
font_family="Arial",
font_color="#646363",
font_size=20,
title_font_family="Arial",
title_font_color="#646363",
legend_title_text=None,
legend=dict(font={"size": 18}, yanchor="bottom", y=0.17, xanchor="left", x=0.04),
)
fig.update_yaxes(
title_text="no. DataCite datasets",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 24}},
range=(0, 2010),
tickformat=".2s",
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
)
fig
9.3.7. Plot ZENODO datasets papers vs. year using plotly.express#
fig = px.bar(
data_frame=df_zenodo,
x="publication_year",
y=df_zenodo.columns[1:],
barmode="relative",
color_discrete_sequence=colors,
)
for i, trace in enumerate(fig.data):
trace.update(name=labels[i])
fig.update_layout(
{"plot_bgcolor": "#FFFFFF", "paper_bgcolor": "#FFFFFF"},
width=900,
height=350,
margin=dict(l=90, r=40, t=30, b=45),
font_family="Arial",
font_color="#646363",
font_size=20,
title_font_family="Arial",
title_font_color="#646363",
legend_title_text=None,
legend=dict(font={"size": 18}, yanchor="bottom", y=0.16, xanchor="left", x=0.04),
)
fig.update_yaxes(
title_text="no. ZENODO datasets",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 24}},
range=(0, 402),
tickformat="000",
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
)
fig
9.4. Plot Figure 1 with combined sub-plots using plotly.graph_objects#
from plotly.subplots import make_subplots
import plotly.graph_objects as go
9.4.1. Rearrange dataframes using pandas.melt to be able to use pandas.DataFrame.groupby#
df_wos_rearranged = df_wos.melt(
id_vars="publication_year", var_name="materials", value_name="no_papers"
)
df_wos_rearranged.head()
| publication_year | materials | no_papers | |
|---|---|---|---|
| 0 | 1996 | nanoparticles | 312 |
| 1 | 1997 | nanoparticles | 454 |
| 2 | 1998 | nanoparticles | 749 |
| 3 | 1999 | nanoparticles | 1022 |
| 4 | 2000 | nanoparticles | 1298 |
df_datacite_rearranged = df_datacite.melt(
id_vars="publication_year", var_name="materials", value_name="no_papers"
)
df_datacite_rearranged.head()
| publication_year | materials | no_papers | |
|---|---|---|---|
| 0 | 2010 | nanoparticles | 17.0 |
| 1 | 2011 | nanoparticles | 36.0 |
| 2 | 2012 | nanoparticles | 30.0 |
| 3 | 2013 | nanoparticles | 52.0 |
| 4 | 2014 | nanoparticles | 148.0 |
df_zenodo_rearranged = df_zenodo.melt(
id_vars="publication_year", var_name="materials", value_name="no_papers"
)
df_zenodo_rearranged.head()
| publication_year | materials | no_papers | |
|---|---|---|---|
| 0 | 2010 | nanoparticles | NaN |
| 1 | 2011 | nanoparticles | NaN |
| 2 | 2012 | nanoparticles | 2.0 |
| 3 | 2013 | nanoparticles | NaN |
| 4 | 2014 | nanoparticles | NaN |
colors_dict = dict(
map(lambda i, j: (i, j), df_wos_rearranged["materials"].unique(), colors)
)
colors_dict
{'nanoparticles': '#1a4a81',
'battery_cathode': '#2166ac',
'photocatalytic': '#4393c3',
'polymers': '#92c5de',
'thermoelectric': '#c2e1f2',
'mofs': '#f4a582',
'biomaterials': '#d6604d',
'2Dmaterials': '#b2182b',
'semiconductor': '#67001f'}
9.4.2. Plot combined figure WoS - DataCite - ZENODO#
First, we set up the combined plot.
data_wos = [
go.Bar(
name=group,
x=dfg["publication_year"],
y=dfg["no_papers"],
marker_color=colors_dict[group],
)
for group, dfg in df_wos_rearranged.groupby(by="materials", sort=False)
]
fig_wos = go.Figure(data=data_wos)
for i, trace in enumerate(fig_wos.data):
trace.update(name=labels[i])
data_datacite = [
go.Bar(
name=group,
x=dfg["publication_year"],
y=dfg["no_papers"],
marker_color=colors_dict[group],
hovertemplate="%{y:.0f}",
)
for group, dfg in df_datacite_rearranged.groupby(by="materials", sort=False)
]
fig_datacite = go.Figure(data=data_datacite)
for i, trace in enumerate(fig_datacite.data):
trace.update(name=labels[i])
data_zenodo = [
go.Bar(
name=group,
x=dfg["publication_year"],
y=dfg["no_papers"],
marker_color=colors_dict[group],
hovertemplate="%{y:.0f}",
)
for group, dfg in df_zenodo_rearranged.groupby(by="materials", sort=False)
]
fig_zenodo = go.Figure(data=data_zenodo)
for i, trace in enumerate(fig_zenodo.data):
trace.update(name=labels[i])
fig = make_subplots(rows=3, cols=1, row_heights=[0.7, 0.3, 0.3], vertical_spacing=0.1)
for t in fig_wos.data:
fig.append_trace(t, row=1, col=1)
for t in fig_datacite.data:
fig.append_trace(t, row=2, col=1)
for t in fig_zenodo.data:
fig.append_trace(t, row=3, col=1)
Then, we make cosmetic edits to the plot.
fig.update_layout(
{"plot_bgcolor": "#FFFFFF", "paper_bgcolor": "#FFFFFF"},
barmode="stack",
width=900,
height=850,
margin=dict(l=100, r=40, t=20, b=45),
font_family="Arial",
font_color="#646363",
font_size=18.9,
title_font_family="Arial",
title_font_color="#646363",
legend_title_text=None,
legend=dict(
{"traceorder": "normal"},
font={"size": 18},
yanchor="bottom",
y=0.68,
xanchor="left",
x=0.04,
),
)
fig.update_traces(showlegend=False, row=2, col=1)
fig.update_traces(showlegend=False, row=3, col=1)
tickvals = [*range(0, 220000, 50000)]
ticktext = ["0k", "50k", "100k", "150k", "200k"]
fig.update_yaxes(
title_text="WoS papers",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 21}},
range=(0, 220000),
tickvals=tickvals,
ticktext=ticktext,
tickformat=".2s",
row=1,
col=1,
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickfont=dict(size=17.9),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
row=1,
col=1,
)
tickvals = [*range(0, 2020, 500)]
ticktext = ["0k", "0.5k", "1.0k", "1.5k", "2.0k"]
fig.update_yaxes(
title_text="DataCite datasets",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 21}},
range=(0, 2020),
tickvals=tickvals,
ticktext=ticktext,
tickformat=".2s",
row=2,
col=1,
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickfont=dict(size=17.9),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
row=2,
col=1,
)
fig.update_yaxes(
title_text="ZENODO datasets",
showgrid=True,
gridcolor="#9D9D9C",
title={"font": {"size": 21}},
range=(0, 2020),
tickvals=tickvals,
ticktext=ticktext,
tickformat=".2s",
row=3,
col=1,
)
fig.update_xaxes(
title_text=None,
linecolor="#9D9D9C",
range=(1995.5, 2023.5),
tickfont=dict(size=17.9),
tickvals=[1996, 1999, 2002, 2005, 2008, 2011, 2014, 2017, 2020, 2023],
row=3,
col=1,
)
fig.add_shape(
type="rect",
xref="x domain",
yref="y domain",
x0=-0.065,
y0=-0.1,
x1=1.02,
y1=0.05,
line_width=0,
fillcolor="#d9d9d9",
opacity=0.3,
layer="above",
)
fig.add_shape(
type="rect",
xref="x domain",
yref="y domain",
x0=-0.065,
y0=-0.75,
x1=1.02,
y1=-0.18,
line_width=0,
fillcolor="#d9d9d9",
opacity=0.25,
layer="below",
)
fig.add_shape(
type="rect",
xref="x domain",
yref="y domain",
x0=-0.065,
y0=-1.41,
x1=1.02,
y1=-0.84,
line_width=0,
fillcolor="#d9d9d9",
opacity=0.25,
layer="below",
)
fig