{"id":26573234,"url":"https://github.com/linsalrob/comparereferences","last_synced_at":"2025-07-12T08:36:11.129Z","repository":{"id":146767974,"uuid":"440388622","full_name":"linsalrob/CompareReferences","owner":"linsalrob","description":"Compare References from Google Scholar and ORCID","archived":false,"fork":false,"pushed_at":"2024-08-25T04:42:42.000Z","size":119,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":4,"default_branch":"main","last_synced_at":"2024-08-25T05:35:34.580Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/linsalrob.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-12-21T04:23:36.000Z","updated_at":"2024-08-25T04:42:45.000Z","dependencies_parsed_at":null,"dependency_job_id":"3ab39960-b2d9-4e61-801e-9fa806d876c1","html_url":"https://github.com/linsalrob/CompareReferences","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FCompareReferences","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FCompareReferences/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FCompareReferences/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/linsalrob%2FCompareReferences/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/linsalrob","download_url":"https://codeload.github.com/linsalrob/CompareReferences/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245040190,"owners_count":20551299,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-03-23T00:39:52.788Z","updated_at":"2025-03-23T00:39:53.304Z","avatar_url":"https://github.com/linsalrob.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Edwards Lab](https://img.shields.io/badge/Bioinformatics-EdwardsLab-03A9F4)](https://edwards.sdsu.edu/research)\n[![DOI](https://www.zenodo.org/badge/440388622.svg)](https://www.zenodo.org/badge/latestdoi/440388622)\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n![GitHub language count](https://img.shields.io/github/languages/count/linsalrob/PyFBA)\n\n\n# CompareReferences\nCompare References from two different sources.\n\n# Why?\n\nWe often need to compare references from two different sources to make sure we are upto\ndate. This is trivial and annoying, until you get a couple of hundred references!\n\nHere is a simple python applet to compare the references for you. \n\n\n# How?\n\nIn this example, we will compare references from Google Scholar and ORCID. However, \nyou are not limited to those two services, you can use anything, you just need to\ndownload the references as `bibtex` format files, which is a widely used\nreference format.\n\n## Step 1. Download your Google Scholar references\n1. Log into your Google Account and head to [Google Scholar](https://scholar.google.com/)\n2. Check the box in the toolbar shown below. This activates a \"hidden\" menu:\u003cbr /\u003e\n[![Google Scholar Toolbar](images/gs1.png)](https://scholar.google.com)\n3. The new menu will appear:\u003cbr /\u003e\n[![Google Scholar Toolbar with Export Options](images/gs2.png)](https://scholar.google.com/)\n4. Choose `EXPORT` and then select `BIBTEX` from the pulldown options:\u003cbr /\u003e\n![Google Scholar Export Options](images/gs3.png)\n5. Choose `Export all my articles` from the menu, and then click the export button:\u003cbr /\u003e\n![Google Scholar Export All Articles](images/gs4.png)\n6. On the next page, right click and choose `Save As`:\u003cbr /\u003e\n![Google Scholar Export All Articles](images/gs5.png)\n7. Save this as a file somewhere you will remember!\n\n## Step 2. Download your ORCID references\n1. Log into your [ORC-ID](https://orcid.org/) page\n2. Scroll down until you see `Works`:\u003cbr /\u003e\n![ORCID Works](images/orcid1.png)\n3. Check the box next to `Select All`:\u003cbr /\u003e\n![ORCID checkbox](images/orcid2.png)\n4. Choose `Export all works` from the `Actions` pop up menu:\u003cbr /\u003e\n![ORCID checkbox](images/orcid3.png)\n5. And then choose `Export selected works to BibTex` from the bottom of the next page:\u003cbr /\u003e\n![ORCID checkbox](images/orcid4.png)\n6. This will download a file, which by default is called `works.bib`\n\n## Compare the References\n\nYou can either download and run the executable, or download this Git repository\nand install the modules.\n\n### Use the prebuilt executable\n\nThis is the easiest way, just download the appropriate executable and use it!\n\n### Use the repository\n\nThis is the safest way, because you can see the code you are running!\n\nTo download the repository follow these simple steps:\n\n```bash\ngit clone https://github.com/linsalrob/CompareReferences.git\ncd CompareReferences\npython3.9 -m venv venv\nsource venv/bin/activate\npip install -r requirements.txt\npython3 src/CompareReferences.py \n```\n\nEither way, you will have the window open to read Google Scholar and ORCID files.\n\n1. Read your Google Scholar file. Choose read Google Scholar from the top menu:\u003cbr /\u003e\n![Import GS](images/cr1.png)\n2. Once you have read that, the button will be inactive and you will see how many references were read from that file.\nClick on the Read ORCID file to do the same for ORCID:\u003cbr /\u003e\n![Import GS](images/cr2.png)\n3. Once you have read both files, you will see the number of references in each and the\ncomparison buttons will be available:\u003cbr /\u003e\n![Import GS](images/cr3.png)\n\n   1. `Compare Both` lists references unique to Google and then references in ORCID\n   2. `Google Not ORCID` lists the references unique to Google\n   3. `ORCID Not Google` lists the references unique to ORCID\n4. You can copy and paste the references, or edit them in this text box\n\n## Now what?\n\nYou will notice that we match references by their titles, and try some (but not much)\nfuzzy matching. However, we are not perfect at matching and would rather tell you\nsome citations that maybe different but are not.\n\nI recommend having the two bibtex files open in a text editor, and then going down \nthe list of unique citations and looking to see if you can find it, or something similar,\nin the bibtex file. Often, I search for a unique name or abbreviation. Most of the time,\nespecially for older papers, the difference is subtle, sometimes punctuation or a word like\n`survey` in one citation that is `analysis` in another. \n\nHowever, often a paper is missing and so you need to add that to the appropriate repository. \nSometimes, of course, (especially with Google), there are papers by other authors\nthat have crept into your list and shouldn't be there. Tsk, tsk!\n\nYou can delete and edit things in the text viewer, but please note that this field is not\nsaved, so any changes will be lost to the ether!\n\nSometimes, like the one shown in this final image, it is a biorXiv paper.\u003cbr /\u003e\n![biorXiv rules and should always be included](images/cr4.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fcomparereferences","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flinsalrob%2Fcomparereferences","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flinsalrob%2Fcomparereferences/lists"}