diff --git a/.buildinfo b/.buildinfo index 6d2b9d54..f5e8c792 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: 0eb54b0ccdc3b6a4f1927e3711242c2a +config: 573f68133def913d49454e1870db5889 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_images/25625797232a27f542077b750655915d865723fcc6c33196ec8304f1c6810542.png b/_images/25625797232a27f542077b750655915d865723fcc6c33196ec8304f1c6810542.png deleted file mode 100644 index 1d77ef37..00000000 Binary files a/_images/25625797232a27f542077b750655915d865723fcc6c33196ec8304f1c6810542.png and /dev/null differ diff --git a/_images/945ddf2113edede5fe534881338f5d02ff8874492377d263c66d8a987c08fddf.png b/_images/945ddf2113edede5fe534881338f5d02ff8874492377d263c66d8a987c08fddf.png new file mode 100644 index 00000000..2d033129 Binary files /dev/null and b/_images/945ddf2113edede5fe534881338f5d02ff8874492377d263c66d8a987c08fddf.png differ diff --git a/_images/gsheets_citations_howitworks.jpg b/_images/gsheets_citations_howitworks.jpg new file mode 100644 index 00000000..4a041ec2 Binary files /dev/null and b/_images/gsheets_citations_howitworks.jpg differ diff --git a/_sources/manipulations/gsheets_citations.md b/_sources/manipulations/gsheets_citations.md index 360a717d..44fa4174 100644 --- a/_sources/manipulations/gsheets_citations.md +++ b/_sources/manipulations/gsheets_citations.md @@ -18,13 +18,11 @@ ``` ## Summary -In many research contexts access to the literature is very important and dealing with its metadata can be time-consuming. +In many research contexts, access to the literature is very important and dealing with its metadata can be time-consuming. The advent of the [Digital Object Identifier](https://www.doi.org/) (DOI) has made it much easier to deal with -citation data for many different types of digital resources. Currently, twelve -[registration agencies](https://www.doi.org/the-community/existing-registration-agencies/) are 'minting' (creating) -DOI's and each has a different scope and size. From a research literature perspective -[CrossRef](https://www.crossref.org/) is the agency that holds DOI's (now -[~150,000,000](https://www.crossref.org/06members/53status.html)) and that is a lot of data to sort through. +citation data for many different types of digital resources. Currently, twelve [registration agencies](https://www.doi.org/the-community/existing-registration-agencies/) are +'minting' (creating) DOI's and each has a different scope and size. From a research literature perspective +[CrossRef](https://www.crossref.org/) is the agency that holds DOI's (now [~150,000,000](https://www.crossref.org/06members/53status.html)) and that is a lot of data to sort through. This tutorial therefore focuses on understanding how you can pull in citation metadata from the CrossRef API, and load it in a Google Sheet, to make it easy (for instance) to create a citation string for a paper. An example of a @@ -33,20 +31,76 @@ and you can make a copy and play around with it. Exploring what it takes to put way to understand the CrossRef schema, the structure of how the data is provided. ## 1 Accessing the CrossRef API -The CrossRef API makes available metadata about journal papers, books and other publication types. Detailed documentation +The CrossRef API makes metadata available about journal papers, books and other publication types. Detailed documentation of the API is available at main URL endpoint, https://api.crossref.org. This is too big to go over in this tutorial, so we will just be focusing on the 'works' endpoint (a partial URL that you can add a DOI to) - in this case -https://api.crossref.org/works/. If you append a DOI to the end of this partial URL and put it in a browser you will -get a JSON file returned (see below). The JSON file is formatted using the [JSONView](https://jsonview.com/) +https://api.crossref.org/works/. If you append a DOI to this partial URL and put it in a browser you will +get a JSON file returned (see below). The JSON file in the image is formatted using the [JSONView](https://jsonview.com/) plugin for Firefox and all the fields have been collapsed to make it easy to see the whole file at http://api.crossref.org/works/10.1515/pac-2018-1010. ![fig](../images/gsheets_citations_crossref_api.jpg) - Caption: JSON output from the Crossref API -The data we need to extra to be able to criteria a citation for this paper is spread throughoout different parts of the -JSON file, so we need to know how to get to these metadata. You can think about accessing information in the JSON file -by using the concept of 'paths' to the data elements. This is the same as the path to a file on your computer, going -down into subdirectories until you reach the file. In this case data we need are at the following paths and +The data we need to extract to be able to create a citation for this paper is spread throughoout different parts of the +JSON file, so we need to know how to get to these metadata elements. You can think about accessing information in the +JSON file by using the concept of 'paths' to the data elements (just like accessing files in a computer). In this case +the data we need are at the following paths: + +- **title**: /message/title +- **author last names**: /message/author/given (for each author) +- **author first names**: /message/author/family (for each author) +- **journal**: /message/container-title + (alternatively if you want the journal abbreviation you can use /message/short-container-title if available) +- **year**: /message/published/date-parts (index 0 in the JSON array) +- **volume**: /message/volume +- **issue**: /message/issue +- **pages**: /message/page (yes singular) + +```{note} +Looking at this you will see that while the data is available, it is not as logically organized as it could be and +there are some formatting issues (for instance the abstract). This is a consequence of both the CrossRef schema for +the JSON output, and the approach to populating the metadata of the publisher. With the focus on open citations in +the research community I hope that this will soon be addressed. +``` + +## 2 Getting and formatting the citation string +In order to create our citation string on the Google sheet we need to implement a call to the CrossRef URL, for the +paper retrieval of these metadata fields and some organization and formating. This is implemented in the Google sheet +in each column, and much of the mechanics is hidden in rows between the showing data. This is all explained in the +'How it works' sheet. + +![fig](../images/gsheets_citations_howitworks.jpg) +Caption: The Google Sheets 'How It Works' sheet + +Let's walk through the code. The Crossref path is in cell B2 and the DOI is added to cell B3. The full path is +created in the Google Sheet function 'CONCAT'. Here is an example call to get the data. + +`=ImportJSON(CONCATENATE('How it works'!$B$2,B3),"/message/title","noInherit,noTruncate,rawHeaders")` + +The Google Sheet 'ImportJSON' addon [function](https://workspace.google.com/marketplace/app/importjson_import_json_data_into_google/782573720506) +takes a URL (first variable) and a path to data (second variable) and optionally +so processing options (third variable). When the Google sheet processes this function the data at the path is put into +the cell below the function. This works easily for the title, journal name, volume, issue and pages. + +In order to process the authors and the year we have to do a little more. For the authors, the data is a JSON array +and thus has to be organized to subsequently be able to be put back together as a string. This is done by loading the +data (up to eight authors) into columns B and C, concatenating these in column D and finally concatenating non-empty +cells in B15. This can be expanded to more authors by adding more space for authors and updating the code to cover +all the author data. + +For the year, as there is no 'year' field, we need to take the publised data parts (year, month, day) as a comma +separated string (B19) and then get the first four characters of that string to get the year. It would be easier if the +'path' could point to specific elements in the array (i.e. /message/published/date-parts/0), but this does not work. + +Finally, our goal of a citation string is implemented in B27, by concatenating the fields above with some extra +formatting. In the 'Worksheet' sheet all the mechanics are hidden and all that is needed is to add a DOI of a +paper in each/any of B2, C2, or D2 (you can copy any of the B,C or D columns across to other columns to process) +metadata for more files. + +## 3 Conclusion +In this brief tutorial you can see how Google Sheets and the ImportJSON addon allows you to process any API data. +Given this example, you can create spreadsheet views fo API data and even integrate data from multiple sources. +The only thing to be aware of is that the more calls to APIs that you make in one sheet the slower the over all +sheet will work, but this of course depends on your access speed, so you may need to optimize how you import the data. diff --git a/datasources/cas_commonchem.html b/datasources/cas_commonchem.html index 862101a2..ccab09c7 100644 --- a/datasources/cas_commonchem.html +++ b/datasources/cas_commonchem.html @@ -1466,193 +1466,10 @@

Handle multiple page results 
---------------------------------------------------------------------------
 KeyboardInterrupt                         Traceback (most recent call last)
-Cell In[37], line 6
-      4 n_detail_data = []
+Cell In[37], line 7
       5 for casrn in n_casrn_list:
-----> 6     n_detail_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
-      7     sleep(1) # !! add a delay between API calls
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/api.py:73, in get(url, params, **kwargs)
-     62 def get(url, params=None, **kwargs):
-     63     r"""Sends a GET request.
-     64 
-     65     :param url: URL for the new :class:`Request` object.
-   (...)
-     70     :rtype: requests.Response
-     71     """
----> 73     return request("get", url, params=params, **kwargs)
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/api.py:59, in request(method, url, **kwargs)
-     55 # By using the 'with' statement we are sure the session is closed, thus we
-     56 # avoid leaving sockets open which can trigger a ResourceWarning in some
-     57 # cases, and look like a memory leak in others.
-     58 with sessions.Session() as session:
----> 59     return session.request(method=method, url=url, **kwargs)
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
-    584 send_kwargs = {
-    585     "timeout": timeout,
-    586     "allow_redirects": allow_redirects,
-    587 }
-    588 send_kwargs.update(settings)
---> 589 resp = self.send(prep, **send_kwargs)
-    591 return resp
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
-    700 start = preferred_clock()
-    702 # Send the request
---> 703 r = adapter.send(request, **kwargs)
-    705 # Total elapsed time of the request (approximately)
-    706 elapsed = preferred_clock() - start
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/adapters.py:486, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
-    483     timeout = TimeoutSauce(connect=timeout, read=timeout)
-    485 try:
---> 486     resp = conn.urlopen(
-    487         method=request.method,
-    488         url=url,
-    489         body=request.body,
-    490         headers=request.headers,
-    491         redirect=False,
-    492         assert_same_host=False,
-    493         preload_content=False,
-    494         decode_content=False,
-    495         retries=self.max_retries,
-    496         timeout=timeout,
-    497         chunked=chunked,
-    498     )
-    500 except (ProtocolError, OSError) as err:
-    501     raise ConnectionError(err, request=request)
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:790, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
-    787 response_conn = conn if not release_conn else None
-    789 # Make the request on the HTTPConnection object
---> 790 response = self._make_request(
-    791     conn,
-    792     method,
-    793     url,
-    794     timeout=timeout_obj,
-    795     body=body,
-    796     headers=headers,
-    797     chunked=chunked,
-    798     retries=retries,
-    799     response_conn=response_conn,
-    800     preload_content=preload_content,
-    801     decode_content=decode_content,
-    802     **response_kw,
-    803 )
-    805 # Everything went great!
-    806 clean_exit = True
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:467, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
-    464 try:
-    465     # Trigger any extra validation we need to do.
-    466     try:
---> 467         self._validate_conn(conn)
-    468     except (SocketTimeout, BaseSSLError) as e:
-    469         self._raise_timeout(err=e, url=url, timeout_value=conn.timeout)
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:1096, in HTTPSConnectionPool._validate_conn(self, conn)
-   1094 # Force connect early to allow us to validate the connection.
-   1095 if conn.is_closed:
--> 1096     conn.connect()
-   1098 if not conn.is_verified:
-   1099     warnings.warn(
-   1100         (
-   1101             f"Unverified HTTPS request is being made to host '{conn.host}'. "
-   (...)
-   1106         InsecureRequestWarning,
-   1107     )
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connection.py:642, in HTTPSConnection.connect(self)
-    633 if is_time_off:
-    634     warnings.warn(
-    635         (
-    636             f"System time is way off (before {RECENT_DATE}). This will probably "
-   (...)
-    639         SystemTimeWarning,
-    640     )
---> 642 sock_and_verified = _ssl_wrap_socket_and_match_hostname(
-    643     sock=sock,
-    644     cert_reqs=self.cert_reqs,
-    645     ssl_version=self.ssl_version,
-    646     ssl_minimum_version=self.ssl_minimum_version,
-    647     ssl_maximum_version=self.ssl_maximum_version,
-    648     ca_certs=self.ca_certs,
-    649     ca_cert_dir=self.ca_cert_dir,
-    650     ca_cert_data=self.ca_cert_data,
-    651     cert_file=self.cert_file,
-    652     key_file=self.key_file,
-    653     key_password=self.key_password,
-    654     server_hostname=server_hostname,
-    655     ssl_context=self.ssl_context,
-    656     tls_in_tls=tls_in_tls,
-    657     assert_hostname=self.assert_hostname,
-    658     assert_fingerprint=self.assert_fingerprint,
-    659 )
-    660 self.sock = sock_and_verified.socket
-    661 self.is_verified = sock_and_verified.is_verified
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connection.py:782, in _ssl_wrap_socket_and_match_hostname(sock, cert_reqs, ssl_version, ssl_minimum_version, ssl_maximum_version, cert_file, key_file, key_password, ca_certs, ca_cert_dir, ca_cert_data, assert_hostname, assert_fingerprint, server_hostname, ssl_context, tls_in_tls)
-    779     if is_ipaddress(normalized):
-    780         server_hostname = normalized
---> 782 ssl_sock = ssl_wrap_socket(
-    783     sock=sock,
-    784     keyfile=key_file,
-    785     certfile=cert_file,
-    786     key_password=key_password,
-    787     ca_certs=ca_certs,
-    788     ca_cert_dir=ca_cert_dir,
-    789     ca_cert_data=ca_cert_data,
-    790     server_hostname=server_hostname,
-    791     ssl_context=context,
-    792     tls_in_tls=tls_in_tls,
-    793 )
-    795 try:
-    796     if assert_fingerprint:
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/util/ssl_.py:470, in ssl_wrap_socket(sock, keyfile, certfile, cert_reqs, ca_certs, server_hostname, ssl_version, ciphers, ssl_context, ca_cert_dir, key_password, ca_cert_data, tls_in_tls)
-    467 except NotImplementedError:  # Defensive: in CI, we always have set_alpn_protocols
-    468     pass
---> 470 ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
-    471 return ssl_sock
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/util/ssl_.py:514, in _ssl_wrap_socket_impl(sock, ssl_context, tls_in_tls, server_hostname)
-    511     SSLTransport._validate_ssl_context_for_tls_in_tls(ssl_context)
-    512     return SSLTransport(sock, ssl_context, server_hostname)
---> 514 return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/ssl.py:517, in SSLContext.wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, session)
-    511 def wrap_socket(self, sock, server_side=False,
-    512                 do_handshake_on_connect=True,
-    513                 suppress_ragged_eofs=True,
-    514                 server_hostname=None, session=None):
-    515     # SSLSocket class handles server_hostname encoding before it calls
-    516     # ctx._wrap_socket()
---> 517     return self.sslsocket_class._create(
-    518         sock=sock,
-    519         server_side=server_side,
-    520         do_handshake_on_connect=do_handshake_on_connect,
-    521         suppress_ragged_eofs=suppress_ragged_eofs,
-    522         server_hostname=server_hostname,
-    523         context=self,
-    524         session=session
-    525     )
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/ssl.py:1104, in SSLSocket._create(cls, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname, context, session)
-   1101             if timeout == 0.0:
-   1102                 # non-blocking
-   1103                 raise ValueError("do_handshake_on_connect should not be specified for non-blocking sockets")
--> 1104             self.do_handshake()
-   1105 except:
-   1106     try:
-
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/ssl.py:1382, in SSLSocket.do_handshake(self, block)
-   1380     if timeout == 0.0 and block:
-   1381         self.settimeout(None)
--> 1382     self._sslobj.do_handshake()
-   1383 finally:
-   1384     self.settimeout(timeout)
+      6     n_detail_data.append(requests.get(detail_base_url + "cas_rn=" + casrn).json())
+----> 7     sleep(1) # !! add a delay between API calls
 
 KeyboardInterrupt:
diff --git a/datasources/goldbook_api.html b/datasources/goldbook_api.html index 83124718..344c465c 100644 --- a/datasources/goldbook_api.html +++ b/datasources/goldbook_api.html @@ -587,7 +587,7 @@

Step 5: Use the term code to retrieve its definition

-
{'term': {'id': '01093', 'doi': '10.1351/goldbook.C01093', 'code': 'C01093', 'status': 'current', 'longtitle': 'IUPAC Gold Book - cis-trans isomers', 'title': '<i>cis</i>-<i>trans</i> isomers', 'termversion': '2.3.3', 'lastupdated': '2014-02-24', 'definitions': [{'id': '1', 'text': 'Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]', 'chemicals': [{'type': 'chemimage', 'title': 'molecular structures showing cis/trans isomerism', 'file': 'https://goldbook.iupac.org/img/inline/C01093.png'}], 'links': [{'title': 'Stereoisomeric', 'type': 'internal', 'url': 'https://goldbook.iupac.org/terms/view/S05983'}, {'title': 'olefins', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/O04281'}, {'title': 'cycloalkanes', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01497'}, {'title': 'isomer', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/I03289'}, {'title': 'trans', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01092'}], 'sources': ["PAC, 1996, 68, 2193. 'Basic terminology of stereochemistry (IUPAC Recommendations 1996)' on page 2204 (https://doi.org/10.1351/pac199668122193)"]}], 'referencedin': [{'title': 'Wikipedia - Cis-trans izomerie (cs)', 'url': 'https://cs.wikipedia.org/wiki/Cis-trans_izomerie'}, {'title': 'Wikipedia - Cis-trans izoméria (sk)', 'url': 'https://sk.wikipedia.org/wiki/Cis-trans_izoméria'}, {'title': 'Wikipedia - Cis–trans isomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Cis–trans_isomerism'}, {'title': 'Wikipedia - Isomeria (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria'}, {'title': 'Wikipedia - Isomeria cis-trans (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria_cis-trans'}, {'title': 'Wikipedia - Isomeria geométrica (pt)', 'url': 'https://pt.wikipedia.org/wiki/Isomeria_geométrica'}, {'title': 'Wikipedia - Isomería cis-trans (es)', 'url': 'https://es.wikipedia.org/wiki/Isomería_cis-trans'}, {'title': 'Wikipedia - Talk:Isomer (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Isomer'}, {'title': 'Wikipedia - Talk:Stereoisomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Stereoisomerism'}, {'title': 'Wikipedia - Цис-транс изомеризъм (bg)', 'url': 'https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм'}, {'title': 'Wikipedia - Цис–транс ізомерія (uk)', 'url': 'https://uk.wikipedia.org/wiki/Цис–транс_ізомерія'}, {'title': 'Wikipedia - ایزومری سیس–ترانس (fa)', 'url': 'https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس'}, {'title': 'Wikipedia - 顺反异构 (zh)', 'url': 'https://zh.wikipedia.org/wiki/顺反异构'}], 'links': {'html': 'https://goldbook.iupac.org/terms/view/C01093/html', 'json': 'https://goldbook.iupac.org/terms/view/C01093/json', 'xml': 'https://goldbook.iupac.org/terms/view/C01093/xml', 'plain': 'https://goldbook.iupac.org/terms/view/C01093/plain', 'pdf': 'https://goldbook.iupac.org/terms/view/C01093/pdf'}, 'citation': "Citation: '<i>cis</i>-<i>trans</i> isomers' in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093", 'license': 'The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.', 'collection': 'If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .', 'disclaimer': 'The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.', 'accessed': '2024-03-15T20:24:43+00:00'}}
+
{'term': {'id': '01093', 'doi': '10.1351/goldbook.C01093', 'code': 'C01093', 'status': 'current', 'longtitle': 'IUPAC Gold Book - cis-trans isomers', 'title': '<i>cis</i>-<i>trans</i> isomers', 'termversion': '2.3.3', 'lastupdated': '2014-02-24', 'definitions': [{'id': '1', 'text': 'Stereoisomeric olefins or cycloalkanes (or hetero-analogues) which differ in the positions of atoms (or groups) relative to a reference plane: in the cis-isomer the atoms are on the same side, in the trans-isomer they are on opposite sides. [image: molecular structures showing cis/trans isomerism]', 'chemicals': [{'type': 'chemimage', 'title': 'molecular structures showing cis/trans isomerism', 'file': 'https://goldbook.iupac.org/img/inline/C01093.png'}], 'links': [{'title': 'Stereoisomeric', 'type': 'internal', 'url': 'https://goldbook.iupac.org/terms/view/S05983'}, {'title': 'olefins', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/O04281'}, {'title': 'cycloalkanes', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01497'}, {'title': 'isomer', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/I03289'}, {'title': 'trans', 'type': 'goldify', 'url': 'https://goldbook.iupac.org/terms/view/C01092'}], 'sources': ["PAC, 1996, 68, 2193. 'Basic terminology of stereochemistry (IUPAC Recommendations 1996)' on page 2204 (https://doi.org/10.1351/pac199668122193)"]}], 'referencedin': [{'title': 'Wikipedia - Cis-trans izomerie (cs)', 'url': 'https://cs.wikipedia.org/wiki/Cis-trans_izomerie'}, {'title': 'Wikipedia - Cis-trans izoméria (sk)', 'url': 'https://sk.wikipedia.org/wiki/Cis-trans_izoméria'}, {'title': 'Wikipedia - Cis–trans isomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Cis–trans_isomerism'}, {'title': 'Wikipedia - Isomeria (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria'}, {'title': 'Wikipedia - Isomeria cis-trans (it)', 'url': 'https://it.wikipedia.org/wiki/Isomeria_cis-trans'}, {'title': 'Wikipedia - Isomeria geométrica (pt)', 'url': 'https://pt.wikipedia.org/wiki/Isomeria_geométrica'}, {'title': 'Wikipedia - Isomería cis-trans (es)', 'url': 'https://es.wikipedia.org/wiki/Isomería_cis-trans'}, {'title': 'Wikipedia - Talk:Isomer (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Isomer'}, {'title': 'Wikipedia - Talk:Stereoisomerism (en)', 'url': 'https://en.wikipedia.org/wiki/Talk:Stereoisomerism'}, {'title': 'Wikipedia - Цис-транс изомеризъм (bg)', 'url': 'https://bg.wikipedia.org/wiki/Цис-транс_изомеризъм'}, {'title': 'Wikipedia - Цис–транс ізомерія (uk)', 'url': 'https://uk.wikipedia.org/wiki/Цис–транс_ізомерія'}, {'title': 'Wikipedia - ایزومری سیس–ترانس (fa)', 'url': 'https://fa.wikipedia.org/wiki/ایزومری_سیس–ترانس'}, {'title': 'Wikipedia - 顺反异构 (zh)', 'url': 'https://zh.wikipedia.org/wiki/顺反异构'}], 'links': {'html': 'https://goldbook.iupac.org/terms/view/C01093/html', 'json': 'https://goldbook.iupac.org/terms/view/C01093/json', 'xml': 'https://goldbook.iupac.org/terms/view/C01093/xml', 'plain': 'https://goldbook.iupac.org/terms/view/C01093/plain', 'pdf': 'https://goldbook.iupac.org/terms/view/C01093/pdf'}, 'citation': "Citation: '<i>cis</i>-<i>trans</i> isomers' in IUPAC Compendium of Chemical Terminology, 3rd ed. International Union of Pure and Applied Chemistry; 2006. Online version 3.0.1, 2019. 10.1351/goldbook.C01093", 'license': 'The IUPAC Gold Book is licensed under Creative Commons Attribution-ShareAlike CC BY-SA 4.0 International (https://creativecommons.org/licenses/by-sa/4.0/) for individual terms.', 'collection': 'If you are interested in licensing the Gold Book for commercial use, please contact the IUPAC Executive Director at executivedirector@iupac.org .', 'disclaimer': 'The International Union of Pure and Applied Chemistry (IUPAC) is continuously reviewing and, where needed, updating terms in the Compendium of Chemical Terminology (the IUPAC Gold Book). Users of these terms are encouraged to include the version of a term with its use and to check regularly for updates to term definitions that you are using.', 'accessed': '2024-06-14T19:24:27+00:00'}}
diff --git a/datasources/pubchem_pugrest1.html b/datasources/pubchem_pugrest1.html index 4ca29041..00a449a0 100644 --- a/datasources/pubchem_pugrest1.html +++ b/datasources/pubchem_pugrest1.html @@ -617,7 +617,9 @@

3. Getting Computed Molecular Properties
XLogP            : 1.200
-TPSA             : 63.6
+
+

+
TPSA             : 63.6
diff --git a/datasources/pubchem_pugrest2.html b/datasources/pubchem_pugrest2.html index afdc4beb..696af978 100644 --- a/datasources/pubchem_pugrest2.html +++ b/datasources/pubchem_pugrest2.html @@ -629,9 +629,7 @@

2. Getting chemical names for a given chemical structure
#-- CID 9581
-
- -
PSEUDOEPHEDRINE HYDROCHLORIDE
+PSEUDOEPHEDRINE HYDROCHLORIDE
 Pseudoephedrine Hcl
 345-78-8
 Rhinalair
@@ -688,51 +686,26 @@ 
2. Getting chemical names for a given chemical structure2. Getting chemical names for a given chemical structure
-
Aleve PM
+
#-- CID 77098502
+Aleve PM
 Naproxen sodium/DPH combination
 Diphenhydramine HCl / naproxen sodium
 BAY98-7111
diff --git a/datasources/pubchem_pugrest3.html b/datasources/pubchem_pugrest3.html
index 401944f4..bada11f5 100644
--- a/datasources/pubchem_pugrest3.html
+++ b/datasources/pubchem_pugrest3.html
@@ -711,8 +711,8 @@ 
3. Performing 2-D and 3-D similarity search
-
562
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'164701758', '164701760', '164701766', '164701772', '164701773', '164701775', '164701776', '164701777', '164701789', '164701794', '164701800', '164701805', '164701807', '164701812', '164701813', '164701815', '164701816', '164701817', '164701818', '164701819', '164701821', '164766036', '164766041', '164785132', '164850071', '164971185', '165179472', '165179485', '165179486', '165179488', '166149062', '166149074', '166149077', '166149089', '166149094', '166149137', '166156664', '166156828', '166156836', '166157017', '166157043', '166157215', '166157269', '166494662', '166494843', '166537627', '166840326', '166840392', '166840457', '166840466', '166840731', '166891533', '166891547', '166891596', '166891665', '166893182', '166893274', '166893275', '166893276', '166893348', '166893351', '167065080', '167065082', '167065154', '167065160', '167094315', '167094316', '167094334', '167094341', '167203581', '167206597', '167206598', '167206599', '167206807', '167207061', '167229685', '167251496', '167331630', '167331639', '167338845', '167338850', '167338914', '167338917', '167338943', '167480975', '167480997', '167481005', '167481033', '167481034', '167481037', '167481072', '167481103', '167481130', '167481158', '167481199', '167481201', '167481202', '167481210', '167481232', '167481234', '167481250', '167481257', '167481266', '167481309', '167481324', '167481327', '167481349', '167481356', '167481364', '167481374', '167481379', '167481386', '167481398', '167481400', '167481430', '167481462', '167481474', '167481480', '167481535', '167481542', '167481547', '167481557', '167481565', '167481566', '167481575', '167481608', '167481637', '167481640', '167481663', '167481675', '167481747', '167481808', '167481821', '167481860', '167481876', '167481880', '167481900', '167481908', '167481917', '167481924', '167481927', '167481929', '167481944', '167481972', '167481999', '167482005', '167482039', '167482043', '167482074', '167482083', '167482106', '167482167', '167482178', '167482205', '167482212', '167482213', '167482218', '167482232', '167482240', '167482261', '167482283', '167482292', '167482295', '167482314', '167482317', '167518190', '167521394', '167579537', '168142141', '168142152', '168142166', '168142167', '168142213', '168750579', '168750586', '168750590', '168750593', '168878798', '168941969', '168942044', '169084224', '169122295', '169193197', '169193261', '169193357', '169193547', '169193552', '169193733', '169193751', '169193754', '169193839', '169193963', '169193968', '169194030', '169194114', '169194124', '169194140', '169194186', '169194204', '169194236', '169194258', '169194427', '169240696', '169240697', '169240701', '169283836', '169283867', '169283881', '169291133', '169436363', '170552067', '170552068', '170631558', '170631565', '170631680', '170631745', '170701828', '170701834', '170701836', '170701844', '170701848', '170701854', '170701858', '171108715', '171108717', '163285815', '163341926', '166149063', '166156829', '167278770', '167481104', '167481950', '167481970', '167482299', '167482300', '168010016', '168301133', '168310836', '168310837', '168878799', '169240702', '169436361', '169595627', '169595871', '169595876', '169595900', '169595902', '169595937', '169595991', '169595994', '169597577', '169655654', '169655658', '169655661', '169655677', '169655713', '169655746', '169655747', '169655787', '169655789', '169676887', '169686050', '169686051', '169707956', '169707957', '169732235', '169732236', '169734644', '169735016', '169737661', '169816596', '169860851', '169860855', '169860863', '169860866', '169860882', '169861043', '169861121', '169861122', '169861123', '169861126', '169861127', '169861128', '169861209', '169861410', '169861544', '169861545', '169861547', '169861552', '169861641', '169861643', '169861899', '169861924', '169862040', '169878303', '169878305', '169878307', '169878308', '169878350', '169878352', '169878353', '169878366', '169878439', '169878441', '169878442', '169878445', '169878446', '169878447', '169878448', '169878449', '169878451', '169878452', '169878453', '169878454', '169878455', '169878511', '169878512', '169878513', '169878514', '169878517', '169878631', '169878890', '169907886', '169907978', '169914647', '169914666', '169914913', '169966328', '169979396', '169979540', '169989970', '169994700', '169994701', '169994702', '169994703', '169994705', '169994706', '169994745', '169994895', '169994956', '169995108', '169995153', '169995154', '169995401', '169995678', '169995679', '169995904', '170005512', '170036051', '170036248', '170036541', '170036799', '170036842', '170036848', '170036858', '170036928', '170036943', '170036979', '170037210', '170037247', '170038496', '170052972', '170052975', '170053129', '170053614', '170053627', '170053669', '170054633', '170054800', '170060745', '170060748', '170151866', '170164590', '170164688', '170164691', '170164767', '170165331', '170165489', '170165491', '170165562', '170165698', '170165798', '170166112', '170166207', '170166212', '170166479', '170166597', '170166774', '170166889', '170166912', '170166968', '170167024', '170167108', '170167453', '170167521', '170167675', '170167936', '170168021', '170203998', '170404012', '171379688', '162712468', '162712490', '162712506', '163283283', '163362019', '164701798', '164701802', '164850073', '164850290', '166157157', '166964883', '166964886', '166964888', '166964890', '166964899', '166964903', '166964904', '166964908', '166964913', '166986000', '166986065', '166986067', '166986077', '167203321', '167481489', '167482130', '167574477', '167574478', '168093174', '168154285', '168993735', '169084219', '169084221', '169084228', '169095061', '169193396', '169193437', '169193895', '169193967', '169193984', '169194217', '169194293', '169194319', '169194330', '169194348', '166642632', '167537951', '167674037', '168476190', '168993728', '169595592', '169595872', '169595897', '169595998', '169655830', '169728040', '169728041', '169728431', '169728432', '169736642', '169736643', '169862121', '169878349', '169914451', '169915447', '169915455', '169915574', '169995311', '170014641', '170036241', '170036499', '170036602', '170052965', '170053029', '170053921', '170080981', '170164555', '170165348', '170165794', '170165926', '170166075', '170167073', '170167420', '170167651', '170167680', '170168510', '170168543', '170200729', '170201013', '170291885', '171394959']
 

 

 

@@ -728,8 +728,8 @@ 
3. Performing 2-D and 3-D similarity search
-
41
-['155903259', '167331698', '166157194', '163362001', '162396459', '169240696', '168301133', '168290284', '167094316', '167094315', '167065082', '164701818', '164701813', '164701812', '164701760', '164701758', '164040179', '163362031', '163362005', '163361849', '170701834', '170404012', '170060748', '169914913', '169878307', '169878303', '169861545', '169861544', '169861123', '169861121', '169860863', '169860851', '169707957', '169707956', '169686051', '169595994', '169240702', '163341926', '163285815', '166642632', '168476190']
+
42
+['155903259', '162396459', '163362001', '166157194', '167331698', '168290284', '163361849', '163362005', '163362031', '164040179', '164701758', '164701760', '164701812', '164701813', '164701818', '167065082', '167094315', '167094316', '169240696', '170701834', '163285815', '163341926', '168301133', '169240702', '169595994', '169686051', '169707956', '169707957', '169860851', '169860863', '169861121', '169861123', '169861544', '169861545', '169878303', '169878307', '169914913', '170060748', '170404012', '166642632', '168476190', '171394959']
 

 

 

@@ -746,46 +746,47 @@ 
3. Performing 2-D and 3-D similarity search
 
"CID","HeavyAtomCount","MolecularFormula","IsomericSMILES"
 155903259,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-167331698,34,"C23H33F2N5O4","CC(C)C[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)F"
-166157194,34,"C23H33F2N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-163362001,35,"C23H32F3N5O4","CC(C)C[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)(F)F"
 162396459,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@H](C[C@@H]3CCNC3=O)C#N)C"
-169240696,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)N([C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)C(F)(F)F)C(=O)N)C"
-168301133,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+163362001,35,"C23H32F3N5O4","CC(C)C[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)(F)F"
+166157194,34,"C23H33F2N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+167331698,34,"C23H33F2N5O4","CC(C)C[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)F"
 168290284,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@H]3CCNC3=O)C#N)C"
-167094316,35,"C23H32F3N5O4","CC1([C@H]2C1CN([C@@H]2C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C"
-167094315,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-167065082,35,"C23H32F3N5O4","CC1(C2C1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-164701818,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@H](C[C@@H]3CCNC3=O)C#N)C"
-164701813,35,"C23H32F3N5O4","CC(C)C[C@@H](C(=O)N1CC2C(C1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)(F)F"
-164701812,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-164701760,36,"C24H34F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](CC(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-164701758,35,"C23H32F3N5O4","CC(C)[C@@H](C(=O)N1CC2C(C1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)CC(F)(F)F"
-164040179,36,"C24H36F3N5O4","C.CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-163362031,36,"C24H34F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CC(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-163362005,35,"C23H32F3N5O4","CC(C)[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)CC(F)(F)F"
 163361849,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
+163362005,35,"C23H32F3N5O4","CC(C)[C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)CC(F)(F)F"
+163362031,36,"C24H34F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CC(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+164040179,36,"C24H36F3N5O4","C.CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+164701758,35,"C23H32F3N5O4","CC(C)[C@@H](C(=O)N1CC2C(C1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)CC(F)(F)F"
+164701760,36,"C24H34F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](CC(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+164701812,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+164701813,35,"C23H32F3N5O4","CC(C)C[C@@H](C(=O)N1CC2C(C1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)(F)F"
+164701818,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@H](C[C@@H]3CCNC3=O)C#N)C"
+167065082,35,"C23H32F3N5O4","CC1(C2C1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+167094315,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+167094316,35,"C23H32F3N5O4","CC1([C@H]2C1CN([C@@H]2C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C"
+169240696,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)[C@H](C(C)(C)C)N([C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)C(F)(F)F)C(=O)N)C"
 170701834,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NCC[C@H]3C[C@H](NC3=O)C#N)C"
-170404012,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-170060748,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
-169914913,36,"C24H34F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)CC(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-169878307,35,"C23H32F3N5O4","CC1CNC(=O)[C@@H]1C[C@@H](C#N)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)C)NC(=O)C(F)(F)F"
-169878303,36,"C24H34F3N5O4","CC1CNC(=O)[C@@H]1C[C@@H](C#N)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F"
-169861545,37,"C24H35F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-169861544,38,"C25H37F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
-169861123,37,"C24H35F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(CCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
-169861121,38,"C25H37F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
-169860863,37,"C24H35F3N6O4","CC1(C2C1C(N(C2)C(=O)C(CCCN(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
-169860851,38,"C25H37F3N6O4","CC1(C2C1C(N(C2)C(=O)C(CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
-169707957,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
-169707956,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
-169686051,35,"C23H32F3N5O4","CC1([C@H]2C1CN([C@@H]2C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C"
-169595994,35,"C24H35F2N5O4","CC(C)C[C@@H](C(=O)N1C[C@]2([C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)C)NC(=O)C(F)F"
-169240702,35,"C23H32F3N5O4","CC1(C2C1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
-163341926,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
 163285815,35,"C23H32F3N5O4","CC1([C@@H]2[C@@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+163341926,35,"C23H32F3N5O4","CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
+168301133,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+169240702,35,"C23H32F3N5O4","CC1(C2C1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
+169595994,35,"C24H35F2N5O4","CC(C)C[C@@H](C(=O)N1C[C@]2([C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)C)NC(=O)C(F)F"
+169686051,35,"C23H32F3N5O4","CC1([C@H]2C1CN([C@@H]2C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C"
+169707956,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
+169707957,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
+169860851,38,"C25H37F3N6O4","CC1(C2C1C(N(C2)C(=O)C(CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
+169860863,37,"C24H35F3N6O4","CC1(C2C1C(N(C2)C(=O)C(CCCN(C)C)NC(=O)C(F)(F)F)C(=O)NC(CC3CCNC3=O)C#N)C"
+169861121,38,"C25H37F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
+169861123,37,"C24H35F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)C(CCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CC3CCNC3=O)C#N)C"
+169861544,38,"C25H37F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CCCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+169861545,37,"C24H35F3N6O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](CCCN(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+169878303,36,"C24H34F3N5O4","CC1CNC(=O)[C@@H]1C[C@@H](C#N)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F"
+169878307,35,"C23H32F3N5O4","CC1CNC(=O)[C@@H]1C[C@@H](C#N)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)C)NC(=O)C(F)(F)F"
+169914913,36,"C24H34F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)CC(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
+170060748,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(C[C@@H]3CCNC3=O)C#N)C"
+170404012,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1C(N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C"
 166642632,35,"C23H32F3N5O4","[2H]C([2H])([2H])C([C@@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)C#N)C2(C)C)NC(=O)C(F)(F)F)(C([2H])([2H])[2H])C([2H])([2H])[2H]"
 168476190,35,"C23H32F3N5O4","[2H]C1(C[C@H](C(=O)N1)C[C@@H](C#N)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)[2H]"
+171394959,35,"C23H32F3N5O4","CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@H](C[C@H]3CCNC3=O)C#N)C"
 

 

 

@@ -819,7 +820,7 @@ 
5. Performing substructure/superstructure search
-
41224
+
41285
 

 

 

@@ -833,7 +834,7 @@ 
5. Performing substructure/superstructure search
-
6839
+
6853
 

 

 

@@ -850,7 +851,7 @@ 
7. Molecular Formula search
-
1568
+
1571
 

 

 

@@ -881,15 +882,15 @@ 
7. Molecular Formula search
 
['CID', 'MolecularFormula', 'IsomericSMILES']
 2723872 	 C6H12O6 	 C1[C@H]([C@H]([C@@H](C(O1)(CO)O)O)O)O
-64689 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
 892 	 C6H12O6 	 C1(C(C(C(C(C1O)O)O)O)O)O
-79025 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
-24310 	 C6H12O6 	 C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
 5793 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O
-439709 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
-439312 	 C6H12O6 	 C1[C@H]([C@@H]([C@@H](C(O1)(CO)O)O)O)O
-18950 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@@H](C(O1)O)O)O)O)O
+107526 	 C6H12O6 	 C([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)O
 6036 	 C6H12O6 	 C([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O
+64689 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
+439312 	 C6H12O6 	 C1[C@H]([C@@H]([C@@H](C(O1)(CO)O)O)O)O
+24310 	 C6H12O6 	 C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
+439353 	 C6H12O6 	 C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
+439709 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
 

 

 

@@ -902,7 +903,7 @@ 
7. Molecular Formula search
-
3317
+
3319
 

 

 

@@ -932,15 +933,15 @@ 
7. Molecular Formula search
 
['CID', 'MolecularFormula', 'IsomericSMILES']
 2723872 	 C6H12O6 	 C1[C@H]([C@H]([C@@H](C(O1)(CO)O)O)O)O
-64689 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
 892 	 C6H12O6 	 C1(C(C(C(C(C1O)O)O)O)O)O
-79025 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)O
-24310 	 C6H12O6 	 C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
 5793 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H](C(O1)O)O)O)O)O
-439709 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
-439312 	 C6H12O6 	 C1[C@H]([C@@H]([C@@H](C(O1)(CO)O)O)O)O
-18950 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@@H](C(O1)O)O)O)O)O
+107526 	 C6H12O6 	 C([C@H]([C@H]([C@@H]([C@H](C=O)O)O)O)O)O
 6036 	 C6H12O6 	 C([C@@H]1[C@@H]([C@@H]([C@H](C(O1)O)O)O)O)O
+64689 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
+439312 	 C6H12O6 	 C1[C@H]([C@@H]([C@@H](C(O1)(CO)O)O)O)O
+24310 	 C6H12O6 	 C1[C@H]([C@H]([C@@H]([C@](O1)(CO)O)O)O)O
+439353 	 C6H12O6 	 C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)O
+439709 	 C6H12O6 	 C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)O
 

 

 

diff --git a/datasources/pubchem_pugview.html b/datasources/pubchem_pugview.html
index cc33ffed..65669e5c 100644
--- a/datasources/pubchem_pugview.html
+++ b/datasources/pubchem_pugview.html
@@ -577,7 +577,7 @@ 
1. Annotations for a PubChem compound record.
-
{'ReferenceNumber': 37,
+
{'ReferenceNumber': 41,
  'Description': 'PEER REVIEWED',
  'Reference': ["O'Neil, M.J. (ed.). The Merck Index - An Encyclopedia of Chemicals, Drugs, and Biologicals. Cambridge, UK:  Royal Society of Chemistry, 2013., p. 593"],
  'Value': {'StringWithMarkup': [{'String': '2.47cP at 20 °C'}]}}
@@ -913,12 +934,6 @@ 
3.3 Multi-page annotations
Getting data for page 5
 

 

-
Getting data for page 10
-

-

-
Getting data for page 15
-

-

 
---------------------------------------------------------------------------
 KeyboardInterrupt                         Traceback (most recent call last)
 Cell In[20], line 10
@@ -928,7 +943,7 @@ 
3.3 Multi-page annotations     12 if page_curr % 5 == 0 :
      13     print("Getting data for page", page_curr)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/api.py:73, in get(url, params, **kwargs)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/requests/api.py:73, in get(url, params, **kwargs)
      62 def get(url, params=None, **kwargs):
      63     r"""Sends a GET request.
      64 
@@ -938,14 +953,14 @@ 
3.3 Multi-page annotations     71     """
 ---> 73     return request("get", url, params=params, **kwargs)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/api.py:59, in request(method, url, **kwargs)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/requests/api.py:59, in request(method, url, **kwargs)
      55 # By using the 'with' statement we are sure the session is closed, thus we
      56 # avoid leaving sockets open which can trigger a ResourceWarning in some
      57 # cases, and look like a memory leak in others.
      58 with sessions.Session() as session:
 ---> 59     return session.request(method=method, url=url, **kwargs)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/requests/sessions.py:589, in Session.request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
     584 send_kwargs = {
     585     "timeout": timeout,
     586     "allow_redirects": allow_redirects,
@@ -954,14 +969,14 @@ 
3.3 Multi-page annotations--> 589 resp = self.send(prep, **send_kwargs)
     591 return resp
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/requests/sessions.py:703, in Session.send(self, request, **kwargs)
     700 start = preferred_clock()
     702 # Send the request
 --> 703 r = adapter.send(request, **kwargs)
     705 # Total elapsed time of the request (approximately)
     706 elapsed = preferred_clock() - start
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/requests/adapters.py:486, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/requests/adapters.py:486, in HTTPAdapter.send(self, request, stream, timeout, verify, cert, proxies)
     483     timeout = TimeoutSauce(connect=timeout, read=timeout)
     485 try:
 --> 486     resp = conn.urlopen(
@@ -980,7 +995,7 @@ 
3.3 Multi-page annotations    500 except (ProtocolError, OSError) as err:
     501     raise ConnectionError(err, request=request)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:790, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:790, in HTTPConnectionPool.urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, preload_content, decode_content, **response_kw)
     787 response_conn = conn if not release_conn else None
     789 # Make the request on the HTTPConnection object
 --> 790 response = self._make_request(
@@ -1000,48 +1015,48 @@ 
3.3 Multi-page annotations    805 # Everything went great!
     806 clean_exit = True
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:536, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/urllib3/connectionpool.py:536, in HTTPConnectionPool._make_request(self, conn, method, url, body, headers, retries, timeout, chunked, response_conn, preload_content, decode_content, enforce_content_length)
     534 # Receive the response from the server
     535 try:
 --> 536     response = conn.getresponse()
     537 except (BaseSSLError, OSError) as e:
     538     self._raise_timeout(err=e, url=url, timeout_value=read_timeout)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/urllib3/connection.py:461, in HTTPConnection.getresponse(self)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/urllib3/connection.py:461, in HTTPConnection.getresponse(self)
     458 from .response import HTTPResponse
     460 # Get the response from http.client.HTTPConnection
 --> 461 httplib_response = super().getresponse()
     463 try:
     464     assert_header_parsing(httplib_response.msg)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/http/client.py:1390, in HTTPConnection.getresponse(self)
-   1388 try:
-   1389     try:
--> 1390         response.begin()
-   1391     except ConnectionError:
-   1392         self.close()
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/http/client.py:1395, in HTTPConnection.getresponse(self)
+   1393 try:
+   1394     try:
+-> 1395         response.begin()
+   1396     except ConnectionError:
+   1397         self.close()
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/http/client.py:325, in HTTPResponse.begin(self)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/http/client.py:325, in HTTPResponse.begin(self)
     323 # read until we get a non-100 response
     324 while True:
 --> 325     version, status, reason = self._read_status()
     326     if status != CONTINUE:
     327         break
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/http/client.py:286, in HTTPResponse._read_status(self)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/http/client.py:286, in HTTPResponse._read_status(self)
     285 def _read_status(self):
 --> 286     line = str(self.fp.readline(_MAXLINE + 1), "iso-8859-1")
     287     if len(line) > _MAXLINE:
     288         raise LineTooLong("status line")
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/socket.py:706, in SocketIO.readinto(self, b)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/socket.py:706, in SocketIO.readinto(self, b)
     704 while True:
     705     try:
 --> 706         return self._sock.recv_into(b)
     707     except timeout:
     708         self._timeout_occurred = True
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/ssl.py:1314, in SSLSocket.recv_into(self, buffer, nbytes, flags)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/ssl.py:1314, in SSLSocket.recv_into(self, buffer, nbytes, flags)
    1310     if flags != 0:
    1311         raise ValueError(
    1312           "non-zero flags not allowed in calls to recv_into() on %s" %
@@ -1050,7 +1065,7 @@ 
3.3 Multi-page annotations   1315 else:
    1316     return super().recv_into(buffer, nbytes, flags)
 
-File /opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/ssl.py:1166, in SSLSocket.read(self, len, buffer)
+File /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/ssl.py:1166, in SSLSocket.read(self, len, buffer)
    1164 try:
    1165     if buffer is not None:
 -> 1166         return self._sslobj.read(len, buffer)
diff --git a/manipulations/computing_inchis.html b/manipulations/computing_inchis.html
index e5fe6b70..750e71c2 100644
--- a/manipulations/computing_inchis.html
+++ b/manipulations/computing_inchis.html
@@ -539,7 +539,7 @@ 
1.2 Create a Molecular Object from SMILES
-
<rdkit.Chem.rdchem.Mol object at 0x75903f5a5070>
+
<rdkit.Chem.rdchem.Mol object at 0x7f658ffb11c0>
 

 

 

@@ -620,7 +620,7 @@ 
1.4 Calculate InChIs for a List of Molecules
-
[<rdkit.Chem.rdchem.Mol object at 0x75903f5a5540>, <rdkit.Chem.rdchem.Mol object at 0x75903f5a5620>, <rdkit.Chem.rdchem.Mol object at 0x75903f5a5a10>, <rdkit.Chem.rdchem.Mol object at 0x75903f5a5a80>, <rdkit.Chem.rdchem.Mol object at 0x75903f5a5af0>, <rdkit.Chem.rdchem.Mol object at 0x75903f5a5b60>]
+
[<rdkit.Chem.rdchem.Mol object at 0x7f658ffb1770>, <rdkit.Chem.rdchem.Mol object at 0x7f658ffb17e0>, <rdkit.Chem.rdchem.Mol object at 0x7f658ffb1b60>, <rdkit.Chem.rdchem.Mol object at 0x7f658ffb1bd0>, <rdkit.Chem.rdchem.Mol object at 0x7f658ffb1c40>, <rdkit.Chem.rdchem.Mol object at 0x7f658ffb1cb0>]
 

 

 

@@ -779,7 +779,7 @@ 
2.4 Calculate InChIs for a List of Molecules
-
[<openbabel.pybel.Molecule object at 0x75903e5a1610>, <openbabel.pybel.Molecule object at 0x75903e5a1250>, <openbabel.pybel.Molecule object at 0x75903e5a1dd0>, <openbabel.pybel.Molecule object at 0x75903e5a1350>, <openbabel.pybel.Molecule object at 0x75903e5a1010>, <openbabel.pybel.Molecule object at 0x75903e5a0f50>]
+
[<openbabel.pybel.Molecule object at 0x7f658e752490>, <openbabel.pybel.Molecule object at 0x7f658e751f10>, <openbabel.pybel.Molecule object at 0x7f658e751b50>, <openbabel.pybel.Molecule object at 0x7f658e751a10>, <openbabel.pybel.Molecule object at 0x7f658e751990>, <openbabel.pybel.Molecule object at 0x7f658e7518d0>]
 

 

 

diff --git a/manipulations/dataset_search.html b/manipulations/dataset_search.html
index 027d81a6..1745d9e0 100644
--- a/manipulations/dataset_search.html
+++ b/manipulations/dataset_search.html
@@ -637,6 +637,10 @@ 
1.2 - Search for sources that have ‘curation efforts’1.2 - Search for sources that have ‘curation efforts’1.2 - Search for sources that have ‘curation efforts’
-
{'success': True, 'jwt': 'eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzEwNTM0MzczLCJleHAiOjE3MTA2MjA3NzN9.BC3BQTaB2p0nXjJy6NFXlOuljvRXvc7wSUc7-QHrnXk', 'username': 'ChemCookbook', 'id': 8509, 'role': 'user', 'profile_type': 'none', 'watched_records': [], 'is_curator': False, 'is_super_curator': False, 'third_party': False, 'expiry': 1710620773, 'message': 'Authentication successful'}
+
{'success': True, 'jwt': 'eyJhbGciOiJIUzI1NiJ9.eyJqdGkiOiI0YjVkNzQyMi1hOTg3LTRlZWYtYjQyYi1hN2U3Yjc2MTM0ZTEiLCJzdWIiOiI4NTA5Iiwic2NwIjoidXNlciIsImF1ZCI6bnVsbCwiaWF0IjoxNzE4MzkzMTUzLCJleHAiOjE3MTg0Nzk1NTN9.gxVkoZ_NwvyUqP-CQNu8w1hVNC0qYljLV0ybOu3C4eg', 'username': 'ChemCookbook', 'id': 8509, 'role': 'user', 'profile_type': 'none', 'watched_records': [], 'is_curator': False, 'is_super_curator': False, 'third_party': False, 'expiry': 1718479553, 'message': 'Authentication successful'}
 

 

 

@@ -1091,8 +1111,7 @@ 
2.2 - Make the API request2.3 - Output the data in a presentable format
 
FAIRsharing record for: Portable reduced-precision binary format for trajectories produced by GROMACS package.: https://fairsharing.org/10.25504/FAIRsharing.cb1adb
 FAIRsharing record for: Chemistry: https://fairsharing.org/fairsharing_records/3524
+FAIRsharing record for: Royal Society of Chemistry - Data policy: https://fairsharing.org/10.25504/FAIRsharing.egbgwm
 FAIRsharing record for: Chemistry vocabulary: https://fairsharing.org/10.25504/FAIRsharing.TrcBD2
 FAIRsharing record for: EMODnet Chemistry: https://fairsharing.org/10.25504/FAIRsharing.KOiDmy
-FAIRsharing record for: Royal Society of Chemistry - Data policy: https://fairsharing.org/10.25504/FAIRsharing.egbgwm
 FAIRsharing record for: MINAS - A Database of Metal Ions in Nucleic AcidS: https://fairsharing.org/10.25504/FAIRsharing.wqtfkv
 FAIRsharing record for: ChemSpider: https://fairsharing.org/10.25504/FAIRsharing.96f3gm
 FAIRsharing record for: ioChem-BD: https://fairsharing.org/10.25504/FAIRsharing.lwW6a1
-FAIRsharing record for: Swedish Ocean Archive: https://fairsharing.org/10.25504/FAIRsharing.npf403
 FAIRsharing record for: Beilstein Journal of Organic Chemistry: https://fairsharing.org/10.25504/FAIRsharing.7GA79k
+FAIRsharing record for: EPA Comptox Chemicals Dashboard: https://fairsharing.org/10.25504/FAIRsharing.tfj7gt
 FAIRsharing record for: CAS Registry Number: https://fairsharing.org/10.25504/FAIRsharing.r7Kwy7
 FAIRsharing record for: Chemical Markup Language: https://fairsharing.org/10.25504/FAIRsharing.3mdt9n
-FAIRsharing record for: CHARMM Card File Format: https://fairsharing.org/10.25504/FAIRsharing.7hp91k
+FAIRsharing record for: Elsevier / American Society for Biochemistry and Molecular Biology - Journal of Biological Chemistry - Data Policy: https://fairsharing.org/fairsharing_records/5290
 FAIRsharing record for: IUPAC International Chemical Identifier: https://fairsharing.org/10.25504/FAIRsharing.ddk9t9
-FAIRsharing record for: Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics: https://fairsharing.org/10.25504/FAIRsharing.207caf
-FAIRsharing record for: Dot Bracket Notation (DBN) - Vienna Format: https://fairsharing.org/10.25504/FAIRsharing.4xrzw1
+FAIRsharing record for: NFDI4Chem : https://fairsharing.org/fairsharing_records/5027
+FAIRsharing record for: CHARMM Card File Format: https://fairsharing.org/10.25504/FAIRsharing.7hp91k
 FAIRsharing record for: Name Reaction Ontology: https://fairsharing.org/10.25504/FAIRsharing.w4tncg
 FAIRsharing record for: Molecular Process Ontology: https://fairsharing.org/10.25504/FAIRsharing.mct09a
 FAIRsharing record for: Chemical Methods Ontology: https://fairsharing.org/10.25504/FAIRsharing.9j4wh2
-FAIRsharing record for: NFDI4Chem : https://fairsharing.org/fairsharing_records/5027
+FAIRsharing record for: Dot Bracket Notation (DBN) - Vienna Format: https://fairsharing.org/10.25504/FAIRsharing.4xrzw1
+FAIRsharing record for: Swedish Ocean Archive: https://fairsharing.org/10.25504/FAIRsharing.npf403
+FAIRsharing record for: Allotrope Data Format: https://fairsharing.org/10.25504/FAIRsharing.26e0d8
 FAIRsharing record for: Chemical Abstracts Service Common Chemistry: https://fairsharing.org/10.25504/FAIRsharing.e5c86e
 FAIRsharing record for: Geological and Environmental Reference Materials: https://fairsharing.org/10.25504/FAIRsharing.219aec
-FAIRsharing record for: MolMeDB: Molecules on Membranes Database: https://fairsharing.org/10.25504/FAIRsharing.CWzk3C
-FAIRsharing record for: Joint Committee on Atomic and Molecular Physical data - working group on Data eXchange: https://fairsharing.org/10.25504/FAIRsharing.v8nve2
-FAIRsharing record for: IUPAC Periodic Table of the Elements: https://fairsharing.org/10.25504/FAIRsharing.92473c
+FAIRsharing record for: Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics: https://fairsharing.org/10.25504/FAIRsharing.207caf
 

 

 

diff --git a/manipulations/gsheets_citations.html b/manipulations/gsheets_citations.html
index 3fc4ee83..81f2cf85 100644
--- a/manipulations/gsheets_citations.html
+++ b/manipulations/gsheets_citations.html
@@ -401,6 +401,8 @@ 
 Contents 

                 
             
         

@@ -446,13 +448,11 @@ 
Importing JSON Citation Data from an API into Google Sheets
 
Summary#

-
In many research contexts access to the literature is very important and dealing with its metadata can be time-consuming.
+
In many research contexts, access to the literature is very important and dealing with its metadata can be time-consuming.
 The advent of the Digital Object Identifier (DOI) has made it much easier to deal with
-citation data for many different types of digital resources.  Currently, twelve
-registration agencies are ‘minting’ (creating)
-DOI’s and each has a different scope and size.  From a research literature perspective
-CrossRef is the agency that holds DOI’s (now

-~150,000,000) and that is a lot of data to sort through.

+citation data for many different types of digital resources.  Currently, twelve registration agencies are
+‘minting’ (creating) DOI’s and each has a different scope and size.  From a research literature perspective
+CrossRef is the agency  that holds DOI’s (now ~150,000,000) and that is a lot of data to sort through.

 
This tutorial therefore focuses on understanding how you can pull in citation metadata from the CrossRef API, and
 load it in a Google Sheet, to make it easy (for instance) to create a citation string for a paper.  An example of a
 sheet that does this is available here,
@@ -461,19 +461,72 @@ 
Summary
 
1 Accessing the CrossRef API#

-
The CrossRef API makes available metadata about journal papers, books and other publication types.  Detailed documentation
+
The CrossRef API makes metadata available about journal papers, books and other publication types.  Detailed documentation
 of the API is available at main URL endpoint, https://api.crossref.org.  This is too big to go over in this tutorial, so
 we will just be focusing on the ‘works’ endpoint (a partial URL that you can add a DOI to) - in this case
-https://api.crossref.org/works/.  If you append a DOI to the end of this partial URL and put it in a browser you will
-get a JSON file returned (see below).  The JSON file is formatted using the JSONView
+https://api.crossref.org/works/.  If you append a DOI to this partial URL and put it in a browser you will
+get a JSON file returned (see below).  The JSON file in the image is formatted using the JSONView
 plugin for Firefox and all the fields have been collapsed to make it easy to see the whole file at
 http://api.crossref.org/works/10.1515/pac-2018-1010.

-
fig

-
Caption: JSON output from the Crossref API

-
The data we need to extra to be able to criteria a citation for this paper is spread throughoout different parts of the
-JSON file, so we need to know how to get to these metadata. You can think about accessing information in the JSON file
-by using the concept of ‘paths’ to the data elements. This is the same as the path to a file on your computer, going
-down into subdirectories until you reach the file. In this case data we need are at the following paths and

+
fig
+Caption: JSON output from the Crossref API

+
The data we need to extract to be able to create a citation for this paper is spread throughoout different parts of the
+JSON file, so we need to know how to get to these metadata elements. You can think about accessing information in the
+JSON file by using the concept of ‘paths’ to the data elements (just like accessing files in a computer). In this case
+the data we need are at the following paths:

+
    
+
  • title: /message/title
    • 
+
  • author last names: /message/author/given (for each author)
    • 
+
  • author first names: /message/author/family (for each author)
    • 
+
  • journal: /message/container-title
+(alternatively if you want the journal abbreviation you can use /message/short-container-title if available)
    • 
+
  • year: /message/published/date-parts (index 0 in the JSON array)
    • 
+
  • volume: /message/volume
    • 
+
  • issue: /message/issue
    • 
+
  • pages: /message/page (yes singular)
    • 
+

+

+
Note

+
Looking at this you will see that while the data is available, it is not as logically organized as it could be and
+there are some formatting issues (for instance the abstract).  This is a consequence of both the CrossRef schema for
+the JSON output, and the approach to populating the metadata of the publisher.  With the focus on open citations in
+the research community I hope that this will soon be addressed.

+

+
+

+
2 Getting and formatting the citation string#

+
In order to create our citation string on the Google sheet we need to implement a call to the CrossRef URL, for the
+paper retrieval of these metadata fields and some organization and formating. This is implemented in the Google sheet
+in each column, and much of the mechanics is hidden in rows between the showing data.  This is all explained in the
+‘How it works’ sheet.

+
fig
+Caption: The Google Sheets ‘How It Works’ sheet

+
Let’s walk through the code.  The Crossref path is in cell B2 and the DOI is added to cell B3.  The full path is
+created in the Google Sheet function ‘CONCAT’.  Here is an example call to get the data.

+
=ImportJSON(CONCATENATE('How it works'!$B$2,B3),"/message/title","noInherit,noTruncate,rawHeaders")

+
The Google Sheet ‘ImportJSON’ addon function
+takes a URL (first variable) and a path to data (second variable) and optionally
+so processing options (third variable).  When the Google sheet processes this function the data at the path is put into
+the cell below the function.  This works easily for the title, journal name, volume, issue and pages.

+
In order to process the authors and the year we have to do a little more.  For the authors, the data is a JSON array
+and thus has to be organized to subsequently be able to be put back together as a string.  This is done by loading the
+data (up to eight authors) into columns B and C, concatenating these in column D and finally concatenating non-empty
+cells in B15.  This can be expanded to more authors by adding more space for authors and updating the code to cover
+all the author data.

+
For the year, as there is no ‘year’ field, we need to take the publised data parts (year, month, day) as a comma
+separated string (B19) and then get the first four characters of that string to get the year.  It would be easier if the
+‘path’ could point to specific elements in the array (i.e. /message/published/date-parts/0), but this does not work.

+
Finally, our goal of a citation string is implemented in B27, by concatenating the fields above with some extra
+formatting.  In the ‘Worksheet’ sheet all the mechanics are hidden and all that is needed is to add a DOI of a
+paper in each/any of B2, C2, or D2 (you can copy any of the B,C or D columns across to other columns to process)
+metadata for more files.

+

+

+
3 Conclusion#

+
In this brief tutorial you can see how Google Sheets and the ImportJSON addon allows you to process any API data.
+Given this example, you can create spreadsheet views fo API data and even integrate data from multiple sources.
+The only thing to be aware of is that the more calls to APIs that you make in one sheet the slower the over all
+sheet will work, but this of course depends on your access speed, so you may need to optimize how you import the data.

 

 
 
@@ -546,6 +599,8 @@ 
1 Accessing the CrossRef API
 
  • Summary
    • 
 
  • 1 Accessing the CrossRef API
    • 
+
  • 2 Getting and formatting the citation string
    • 
+
  • 3 Conclusion
    • 
 
   
    
 
diff --git a/reports/datasources/cas_commonchem.err.log b/reports/datasources/cas_commonchem.err.log
index 27b69a00..b4df2250 100644
--- a/reports/datasources/cas_commonchem.err.log
+++ b/reports/datasources/cas_commonchem.err.log
@@ -1,40 +1,40 @@
 Traceback (most recent call last):
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 780, in _async_poll_for_reply
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 780, in _async_poll_for_reply
     msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 97, in ensure_async
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 97, in ensure_async
     result = await obj
              ^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/jupyter_client/channels.py", line 315, in get_msg
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/jupyter_client/channels.py", line 315, in get_msg
     raise Empty
 _queue.Empty
 
 During handling of the above exception, another exception occurred:
 
 Traceback (most recent call last):
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 1269, in execute
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 1269, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 85, in wrapped
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 85, in wrapped
     return just_run(coro(*args, **kwargs))
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 60, in just_run
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 60, in just_run
     return loop.run_until_complete(coro)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
     return future.result()
            ^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 707, in async_execute
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 707, in async_execute
     await self.async_execute_cell(
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 1006, in async_execute_cell
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 1006, in async_execute_cell
     exec_reply = await self.task_poll_for_reply
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 804, in _async_poll_for_reply
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 804, in _async_poll_for_reply
     error_on_timeout_execute_reply = await self._async_handle_timeout(timeout, cell)
                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 856, in _async_handle_timeout
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 856, in _async_handle_timeout
     raise CellTimeoutError.error_from_timeout_and_cell(
 nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
 The message was: Cell execution timed out.
diff --git a/reports/datasources/pubchem_pugview.err.log b/reports/datasources/pubchem_pugview.err.log
index 53ae3c7b..65f2d39d 100644
--- a/reports/datasources/pubchem_pugview.err.log
+++ b/reports/datasources/pubchem_pugview.err.log
@@ -1,40 +1,40 @@
 Traceback (most recent call last):
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 780, in _async_poll_for_reply
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 780, in _async_poll_for_reply
     msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 97, in ensure_async
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 97, in ensure_async
     result = await obj
              ^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/jupyter_client/channels.py", line 315, in get_msg
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/jupyter_client/channels.py", line 315, in get_msg
     raise Empty
 _queue.Empty
 
 During handling of the above exception, another exception occurred:
 
 Traceback (most recent call last):
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/jupyter_cache/executors/utils.py", line 58, in single_nb_execution
     executenb(
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 1269, in execute
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 1269, in execute
     return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 85, in wrapped
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 85, in wrapped
     return just_run(coro(*args, **kwargs))
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/util.py", line 60, in just_run
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/util.py", line 60, in just_run
     return loop.run_until_complete(coro)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/asyncio/base_events.py", line 654, in run_until_complete
     return future.result()
            ^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 707, in async_execute
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 707, in async_execute
     await self.async_execute_cell(
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 1006, in async_execute_cell
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 1006, in async_execute_cell
     exec_reply = await self.task_poll_for_reply
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 804, in _async_poll_for_reply
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 804, in _async_poll_for_reply
     error_on_timeout_execute_reply = await self._async_handle_timeout(timeout, cell)
                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-  File "/opt/hostedtoolcache/Python/3.11.8/x64/lib/python3.11/site-packages/nbclient/client.py", line 856, in _async_handle_timeout
+  File "/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/nbclient/client.py", line 856, in _async_handle_timeout
     raise CellTimeoutError.error_from_timeout_and_cell(
 nbclient.exceptions.CellTimeoutError: A cell timed out while it was being executed, after 30 seconds.
 The message was: Cell execution timed out.
diff --git a/searchindex.js b/searchindex.js
index b472752c..27ac18df 100644
--- a/searchindex.js
+++ b/searchindex.js
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this Cookbook","About the IUPAC FAIR Chemistry Cookbook Project","Bibliography","Contribute to the Cookbook!","Project Contributors","The Joy of FAIR","Sources of FAIR Chemical Data","CAS Common Chemistry API","Accessing the IUPAC Gold Book API in Python","Data Repository: PubChem","Accessing the Chemical Elements Data from PubChem","PubChem PUG-REST API","Accessing PubChem through PUG-REST - Part I","Accessing PubChem through PUG-REST: Part II","Accessing PubChem through PUG-REST: Part III","Accessing PubChem through PUG-View","Cookbook development","Feedback on the Cookbook","Glossary","Welcome to the IUPAC FAIR Chemistry Cookbook","Manipulating Data within a Digital Environment","Computing InChIs","Finding a Findable Dataset","Importing Chemical Data into Excel","Importing JSON Citation Data from an API into Google Sheets","Using InChI and InChIKey to annotate your chemical entities","FAIR Techniques","Tools for working with FAIR Chemical Data","OPSIN: Open Parser for Systematic IUPAC Nomenclature","Using the OPSIN API in Python","How to use the Cookbook","Use Cases & Workflows","Reuse of Curated Chemical Data","Structured UV/Vis (meta)data for small molecule characterisation","WordFAIR 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this Cookbook","About the IUPAC FAIR Chemistry Cookbook Project","Bibliography","Contribute to the Cookbook!","Project Contributors","The Joy of FAIR","Sources of FAIR Chemical Data","CAS Common Chemistry API","Accessing the IUPAC Gold Book API in Python","Data Repository: PubChem","Accessing the Chemical Elements Data from PubChem","PubChem PUG-REST API","Accessing PubChem through PUG-REST - Part I","Accessing PubChem through PUG-REST: Part II","Accessing PubChem through PUG-REST: Part III","Accessing PubChem through PUG-View","Cookbook development","Feedback on the Cookbook","Glossary","Welcome to the IUPAC FAIR Chemistry Cookbook","Manipulating Data within a Digital Environment","Computing InChIs","Finding a Findable Dataset","Importing Chemical Data into Excel","Importing JSON Citation Data from an API into Google Sheets","Using InChI and InChIKey to annotate your chemical entities","FAIR Techniques","Tools for working with FAIR Chemical Data","OPSIN: Open Parser for Systematic IUPAC Nomenclature","Using the OPSIN API in Python","How to use the Cookbook","Use Cases & Workflows","Reuse of Curated Chemical Data","Structured UV/Vis (meta)data for small molecule characterisation","WordFAIR Chemistry"],titleterms:{"1":[7,8,10,12,13,14,15,21,22,23,24,25,29,33],"2":[7,8,10,12,13,14,15,21,22,23,24,25,29,33],"3":[7,8,10,12,14,15,21,22,23,24,25,29,33],"4":[8,10,12,15,21,25,29,33],"5":[8,14,25,29,33],"6":8,"7":14,"case":[25,31],"float":33,"function":[8,22,33],"import":[7,8,12,21,23,24,25,29],"try":[8,29],The:[5,33],about:[0,1,29],access:[8,10,12,13,14,15,24],accur:25,add:8,affin:10,all:15,an:[14,24,25],anaconda:33,annot:[15,25],api:[7,8,11,12,22,24,29],ar:23,atom:10,audienc:33,authent:22,babel:21,basic:12,between:10,bibliographi:2,boil:10,book:8,ca:[7,25],calcul:21,call:29,can:25,charact:23,characteris:33,check:25,chemic:[6,10,12,13,23,25,27,32],chemistri:[1,7,19,34],citat:24,code:[8,12,33],collect:15,comment:33,common:7,comparison:10,compound:15,comput:[12,21,33],conclus:24,construct:12,contribut:3,contributor:4,cookbook:[0,1,3,16,17,19,30],creat:21,crossref:24,curat:[22,32],d:14,data:[6,7,9,10,12,13,15,20,22,23,24,27,29,32,33],dataset:22,definit:8,densiti:10,detail:7,develop:16,dictionari:33,digit:20,displai:7,doc:33,download:8,draw:[7,25],each:7,effort:22,electron:10,electroneg:10,element:10,encod:23,end:23,energi:10,entiti:25,environ:[20,33],excel:23,exemplar:33,extract:29,fair:[1,5,6,19,22,26,27],fairshar:22,feedback:17,file:[8,23,25,33],find:22,findabl:22,format:[22,23,24,33],formula:[14,29],from:[7,10,15,21,24],get:[12,13,15,24],given:[13,15],glossari:[18,33],gold:8,googl:[23,24,25],handl:7,have:[22,25],head:15,hierarchi:33,how:30,i:[12,25],ident:14,ii:13,iii:14,imag:29,inchi:[14,21,25],inchikei:25,input:14,instal:33,ioniz:10,its:8,iupac:[1,8,19,28],joi:5,json:[8,24],jupyt:33,last:25,let:25,librari:7,line:23,list:[7,21],load:22,loop:7,make:22,manipul:20,mass:10,melt:10,meta:33,method:33,microsoft:23,modul:21,mol:25,molecul:[7,21,33],molecular:[12,14,21,25],multi:15,multipl:[7,15],my:25,name:[13,25],need:[8,12],nomenclatur:28,notebook:33,number:25,object:[21,33],onli:25,open:[21,28],opsin:[28,29],other:[8,15,29],our:25,output:22,packag:[8,12,29,33],page:[7,15],paramet:7,parser:28,part:[12,13,14],perform:14,point:10,potenti:10,present:22,project:[1,4],properti:[12,15],pubchem:[9,10,11,12,13,14,15,22],pug:[11,12,13,14,15],python:[8,12,22,29,33],queri:[14,29],quick:25,rdkit:21,record:[7,15],refer:9,registri:25,report:33,repositori:9,request:[7,12,22],resolv:25,rest:[11,12,13,14],result:7,retriev:[7,8,12],reus:32,rn:[7,25],run:[12,33],s:25,save:7,scenario:[22,25],search:[7,8,14,22],section:15,select:7,setup:7,share:22,sheet:[23,24],similar:14,singl:15,small:33,smile:[14,21,25],some:7,sourc:[6,22],specif:[7,15],step:[8,22,25,29],string:[14,24,25,33],structur:[12,13,33],substanc:[25,29],substructur:14,summari:[23,24],superstructur:14,syntax:12,systemat:28,target:33,techniqu:26,term:[8,33],than:15,thi:[0,12],through:[12,13,14,15],tool:[25,27,33],tutori:9,type:23,unambigu:25,under:15,url:12,us:[8,13,14,21,25,29,30,31,33],uv:33,variabl:33,vi:33,view:15,virtual:33,welcom:19,what:[9,23,33],within:20,word:15,wordfair:34,work:[23,27],workflow:31,you:23,your:[25,33]}})
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diff --git a/tools/opsin_api_jn.html b/tools/opsin_api_jn.html
index f75f0458..68e7c5d9 100644
--- a/tools/opsin_api_jn.html
+++ b/tools/opsin_api_jn.html
@@ -564,7 +564,7 @@ 
    Step 3: Call the OPSIN image API
-../_images/25625797232a27f542077b750655915d865723fcc6c33196ec8304f1c6810542.png
+../_images/945ddf2113edede5fe534881338f5d02ff8874492377d263c66d8a987c08fddf.png
 
    
 
    
 
diff --git a/usecases/uvvis_metadata.html b/usecases/uvvis_metadata.html
index 86632546..914b4588 100644
--- a/usecases/uvvis_metadata.html
+++ b/usecases/uvvis_metadata.html
@@ -705,14 +705,14 @@ 
    4.2 Exemplar code for data reporting
-
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+Requirement already satisfied: numpy in /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages (from jcamp) (1.26.2)
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+Requirement already satisfied: zope.interface in /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages (from datetime->jcamp) (6.1)
+Requirement already satisfied: pytz in /opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages (from datetime->jcamp) (2023.3.post1)
 
    
 
    
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