Academic Gateway

A Guide to Penn State Statistics Course Notes

Thu, 22 Oct 2026 00:00:00 GMT

A Guide to Penn State Statistics Course Notes

The Department of Statistics at Pennsylvania State University makes the notes for several of its courses freely available on STAT Online (online.stat.psu.edu) under the CC BY-NC 4.0 license. The courses include STAT 200 Elementary Statistics, STAT 414 Probability Theory, STAT 501 Regression, STAT 502 Analysis of Variance, and STAT 505 Multivariate Statistics, among others. The notes come with worked examples and Try It! exercises with answers, while assignments, exams, and credit are available only to enrolled students. Based on the official website, this article sets out the software, prerequisites, and recommended study order for each course.

References

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Scope and Rules for Asking Questions on Academia Stack Exchange

Thu, 22 Oct 2026 00:00:00 GMT

Scope and Rules for Asking Questions on Academia Stack Exchange

Academia Stack Exchange is a Q&A site in the Stack Exchange network dedicated to academic life, serving users at every level from students to senior researchers. It answers questions about "how to do academia": graduate study, writing and publishing, peer review, the academic job search, relationships between advisors and students, and similar topics. It does not answer questions about specific subject content, and it does not choose schools or journals for people. Based on the official Help Center, this article outlines the site's scope, its rules for asking and answering, its voting and closing mechanisms, and how its role differs from those of Cross Validated and MathOverflow.

A graduate study group at the University of Washington Information School (iSchool) in Seattle, USA. Photo: Wonderlane; source: Flickr; license: CC BY 2.0.

Scope and Questions That Are Not Accepted

The Help Center's "What topics can I ask about here?" page states that the site is for academics at all levels (from students to senior researchers), and that it also welcomes people who work in or are interested in research-related fields. The topics you can ask about fall into six categories: academic careers; requirements and expectations for students, postdocs, and professors; the inner workings of research departments; academic writing and publishing; studying and teaching at institutions of higher education; and the academic research process. In concrete terms, these include questions about the day-to-day life of master's and doctoral students, submitting and reviewing papers, applying for postdoc and faculty positions, and getting along with advisors or students.

The same page lists what should not be asked: broad, open-ended, or primarily opinion-based questions; the "content" of research and courses itself (the site discusses only the process of research, teaching, and learning, and subject content belongs on the Stack Exchange site for that subject); "shopping questions" that ask people to recommend universities, journals, research topics, and the like; undergraduate admissions; undergraduate life and culture; preparing for non-academic careers; education outside academic settings, such as high school; and overall evaluations of a person's background or chances of admission. The site tour page also lists "the specific regulations of a single university" among the things that should not be asked. For example, "What should I do if the residuals of my regression model are not normally distributed?" is a question about subject content, and "Should I apply to School A or School B?" is a shopping question, so both would be considered off-topic. A typical question here would instead be "While reviewing, I found that a submission duplicates my unpublished work. What should I do?"

Academic conventions vary greatly between countries, institutions, disciplines, and even research groups, so the Help Center asks people to state their (sub)discipline and country in their questions. When a question involves a personal decision, it should focus on "how to make the decision, what the pros and cons are, and what factors need to be considered." Answerers cannot know everything about the asker's situation, and the final decision still rests with the asker. If a question involves serious allegations against others or against oneself, the identities of the people involved, including one's own, should be concealed. Private correspondence should not be made public either; instead, summarize what happened in your own words.

Requirements for Asking and Answering

On asking, "How do I ask a good question?" gives five suggestions: search first, and explain what you found and why it was not enough; stay within the site's topics; give details and context; explain how the question could be useful to others as well; and stay open to answers you don't like, asking answerers to provide sources when necessary. "What types of questions should I avoid asking?" further requires that you ask only answerable questions based on problems you have actually faced, and that you keep the scope reasonable. If you can imagine an entire book being needed to answer the question, you are asking too much. If your motivation is "I would like to participate in a discussion about something," the question is not suitable here. If it is "I would like others to explain something to me," it is usually fine. Subjective questions are not banned outright, but they must be constructive. They should draw out answers that explain "why" and "how," have a fair tone, and encourage people to share experiences rather than simply state positions, and opinions should be backed by facts and references.

After posting, you will often quickly receive comments asking for more information. The Help Center recommends editing the question directly to add that information rather than only replying in the comments, because comments are not prominent enough and may be deleted. The asker can accept one answer but is advised to wait at least a few days, because some users are reluctant to answer questions that already have an accepted answer. The tour page specifically notes that an accepted answer is not necessarily the best one; acceptance only means the answer was helpful to the asker.

On answering, "How do I write a good answer?" asks you to understand the question first. It is fine to say "don't do this," but you should also offer "you could do this instead," and you should explain any limitations, assumptions, and simplifications in your answer. External links should come with context, and the most essential parts should be quoted in case the link breaks. The Help Center also advises against answering questions that are unclear, ask for opinions, have been asked repeatedly, contain multiple questions in one post, or fall outside the scope of academia. When necessary, you can edit the question directly to make it clearer. You may express disagreement, but you should remain polite.

Voting, Reputation, and Closing Mechanisms

According to "Why is voting important?", voting moves useful content to the top and pushes incorrect content down. It also lets users who contribute consistently accumulate reputation and gain more privileges. Asking, answering, and editing require no reputation. At 15 points you can upvote, at 50 points you can comment on any post, and at 125 points you can downvote. One upvote on a question or answer earns its author 10 points, and each downvote costs the author 2 points. A user who downvotes an answer also loses 1 point, while downvoting a question costs nothing. When an answer is accepted, the answerer gains 15 points and the person who accepted it gains 2 points. Reputation earned from voting and editing is capped at 200 points per day. Each user can cast 30 votes on posts per UTC day, plus an additional 10 votes that can be cast only on questions. Answers are sorted by votes by default, and the accepted answer is pinned to the top unless the asker wrote it.

The Academia Stack Exchange question closing and reopening process, compiled from the Help Center page "What does it mean if a question is "closed"?". AI-generated schematic.

Questions that break the rules or need revision are closed. According to the "What does it mean if a question is ‘closed’?" page, users with 3000 reputation can cast close and reopen votes, up to 24 close votes per day. A question is closed once it accumulates 5 close votes, and a single moderator vote is enough to close or reopen it. The close reasons are: duplicate; community-specific reasons (the question falls outside the academic scope defined by the Help Center, or it would be better migrated to another site); needs details or clarity; needs more focus (the post contains multiple questions); and primarily opinion-based. Closed questions can no longer receive answers, and the asker is privately notified of the close reason. The question can still be edited. If a user with enough reputation casts a single reopen vote, or if the asker makes substantive edits that address the close reason, the question enters the reopen review queue. It can be reopened once enough community members agree.

Europe PMC Field Searching and API Usage

Thu, 22 Oct 2026 00:00:00 GMT

Europe PMC Field Searching and API Usage

The European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, which maintains Europe PMC. Photo: Magnus Manske; source: Wikimedia Commons; license: CC BY-SA 3.0.

Europe PMC (europepmc.org) is a free biomedical literature database maintained by EMBL-EBI: it includes all PubMed abstracts, shares full texts with the US PMC, and additionally integrates preprints, patents, clinical guidelines, and funding information. Based on the official manual and API documentation, this article explains how it relates to PubMed, its field search syntax, section-level full-text searching, and text-mining annotations. It also presents 4 search queries and API requests that were actually executed, and covers key points for interpreting results as well as limitations.

Relationship with PubMed and Coverage

Europe PMC and PubMed complement each other; they are not two unrelated sets of data. According to the annual reports published by the Europe PMC team in Nucleic Acids Research, Europe PMC is a member of PMC International, shares full texts with the US PMC and PMC Canada, and provides all PubMed abstracts. The 2020 report further explains that newly received full texts are exchanged daily between the two sites, and that the website merges a PubMed abstract and the corresponding PMC full text onto a single article page. As a result, records that can be found in PubMed generally appear in Europe PMC under the MED source.

Readers familiar with PubMed MeSH searching, introduced previously on this site, should note two differences. First, the official field list has no standalone MeSH field corresponding to PubMed's [mh]: KW: searches both MeSH terms and publisher-supplied keywords, and CHEM: searches MeSH substance terms, so results will be broader than those of a pure subject-heading search. Second, the API's synonym parameter is off by default; only when it is set to true are search terms expanded with MeSH terms and UniProt synonyms, for example expanding aspirin to acetylsalicylic acid. The manual does not say that this is equivalent to PubMed's Automatic Term Mapping or narrower-term explosion, so do not use it as a substitute for MeSH search strategies in systematic searches.

The official Web Service Reference Guide (version 6.9.0, 31 August 2023) uses SRC: source codes to distinguish types of records. Common ones include:

MED: PubMed/MEDLINE records.
PMC: the portion of PubMed Central full texts that have no PubMed record (according to the source description in the Annotations API documentation).
PPR: preprints. The 2020 report states that Europe PMC has included preprint abstracts since 2018, at that time from 15 life-science preprint servers, including bioRxiv, medRxiv, Research Square, and F1000Research, and that in the same year it began including the full texts of COVID-19-related preprints.
PAT: biology-related patents from the European Patent Office (EPO).
HIR: UK clinical guidelines provided by NHS Evidence.
AGR, CBA, ETH, NBK: respectively, Agricola agricultural literature, Chinese Biological Abstracts, British Library EThOS doctoral theses, and Europe PMC Bookshelf books.

Funding information is not a source code but a field attached to literature records. The 2020 report introduced the Grant Finder funding database (which then covered 31 European funders). Links between grants and papers are supplied by funders, by Researchfish, or by authors at submission, and Europe PMC also text-mines grant numbers from the acknowledgments and funding sections of articles. When searching, use the GRANT_AGENCY: (funding agency) and GRANT_ID: (grant number) fields. Note that the manual's source table was written in 2023, so it is unclear whether every source is still being updated. Before relying on a source, you can search it on its own with SRC: and check the index date of its most recent records.

The SciLite interface displaying text-mining annotations in a Europe PMC article, corresponding to the section “REST API and Text-Mining Annotations” below. Figure from the SciLite paper (Wellcome Open Research 1:25); authors: Aravind Venkatesan et al.; source: Wikimedia Commons; license: CC BY 4.0.

Field Search Syntax and Search Queries

Europe PMC search queries take the form “field name:search term”. Phrases go in standard double quotes, terms are combined with AND, OR, NOT, and parentheses, and ranges use square brackets, as in PUB_YEAR:[2020 TO 2024]. The field definitions in the table below come from the appendix of the official reference guide. You can get the complete list of searchable fields by requesting the API's fields module directly; it reflects the current index and is more up to date than the manual.

Field	Purpose	Manual example
`AUTH:`	Author surname, optionally with initials	`AUTH:"einstein G"`
`TITLE:` / `ABSTRACT:` / `TITLE_ABS:`	Title, abstract, title plus abstract	`TITLE_ABS:"african swine fever"`
`AFF:`	Author affiliation	`AFF:"university of cambridge"`
`PUB_YEAR:` / `FIRST_PDATE:`	Publication year, first publication date	`PUB_YEAR:[2000 TO 2001]`
`SRC:`	Source code	`SRC:PPR`
`OPEN_ACCESS:`	Restrict to open access	`OPEN_ACCESS:y`
`IN_EPMC:`	Whether Europe PMC holds the full text	`IN_EPMC:y`
`PUB_TYPE:`	Publication type	`PUB_TYPE:review`
`LICENSE:`	Creative Commons license	`LICENSE:"cc by"`
`GRANT_AGENCY:` / `GRANT_ID:`	Funding agency, grant number	`GRANT_ID:100229`
`METHODS:` / `ACK_FUND:` / `BODY:`	Methods section, acknowledgments and funding section, and body of the full text	`METHODS:"yeast two-hybrid"`
`DISEASE:` / `GENE_PROTEIN:` / `ORGANISM:`	Text-mined diseases, genes/proteins, organisms	`GENE_PROTEIN:gng11`

Complete list of searchable fields: fields module

All of the following queries were actually run through the REST API on 22 October 2026, and the hit counts reflect only that day's results. You can paste the same queries directly into the website's search box.

Example 1: Find preprints on a topic

SRC:PPR AND TITLE:"long covid"

Returned 973 records. The first two came from Research Square and Qeios respectively. Their pubType is preprint, and both isOpenAccess and inEPMC are N, meaning Europe PMC has only metadata for these two records and no full text.

Example 2: Search only in the methods section

METHODS:"propensity score" AND OPEN_ACCESS:y AND PUB_YEAR:[2024 TO 2025]

Returned 14,637 records. METHODS: searches only the “Materials and Methods” section of full texts, so it finds articles that “actually used propensity scores” rather than articles that “mention propensity scores in the title”.

Example 3: Filter by funding agency

GRANT_AGENCY:"Wellcome Trust" AND TITLE_ABS:malaria AND OPEN_ACCESS:y

Returned 4,467 records. Note: the manual's example syntax GRANT_AGENCY:wellcome returned 0 records when tested that day (with or without quotes), whereas GRANT_AGENCY:"Wellcome Trust" on its own returned 219,262 records. The safe approach is to first retrieve one record with resultType=core, check exactly how agency is written in grantsList, and then copy that into your query.

REST API and Text-Mining Annotations

The REST search endpoint is https://www.ebi.ac.uk/europepmc/webservices/rest/search. Sending a GET request from a browser or any HTTP tool is enough, and none of the requests in this article involved registering for or using an API key. The parameters mean the same as in the official manual, and the request field in the REST response echoes them back: query holds the search query; format is json or xml; resultType can be idlist (IDs only), lite (basic metadata, the default), or core (full metadata, including abstract, funding, and full-text links); pageSize defaults to 25, with a maximum of 1000; paging uses cursorMark, where you pass * for the first page and then the nextCursorMark returned by the previous page; synonym defaults to false.

Example 4: Retrieve results in bulk via the API

curl "https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=SRC:PPR%20AND%20TITLE:%22long%20covid%22&format=json&resultType=lite&pageSize=100&cursorMark=*"

To retrieve all results, loop through the pages using nextCursorMark. Below is illustrative code written according to the manual's paging rules; it was not used in this article to fetch a complete result set:

import requests

BASE = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"

def fetch_all(query, page_size=1000, result_type="lite"):
    cursor = "*"
    while True:
        params = {"query": query, "format": "json", "resultType": result_type,
                  "pageSize": page_size, "cursorMark": cursor}
        data = requests.get(BASE, params=params, timeout=60).json()
        results = data["resultList"]["result"]
        yield from results
        next_cursor = data.get("nextCursorMark")
        if not results or not next_cursor or next_cursor == cursor:
            break
        cursor = next_cursor

Full-text searching has clear limits. According to the manual, all Europe PMC content is searchable, but most full texts are restricted by copyright and licensing, and for those articles the API returns only metadata and abstracts. Full-text XML, along with figures, tables, and supplementary materials, can be retrieved only for the open access subset. Section fields such as METHODS:, ACK_FUND:, and BODY: also work only for articles whose full text Europe PMC holds, so abstract-only records will not be matched.

Text-mining annotations are a distinctive feature of Europe PMC compared with PubMed. The 2020 report states that the annotation platform holds about 13 hundred million annotations from 10 providers, covering genes/proteins, diseases, organisms, GO terms, chemicals, database accession numbers, and other types; on the website, SciLite highlights these terms within articles. There are two ways to use them in searches: add HAS_TM:y to a query to restrict results to full-text articles with text-mining results, or use DISEASE:, GENE_PROTEIN:, ORGANISM:, and GOTERM: to search the mined terms directly. To retrieve individual annotations, use the Annotations API.

The Annotations API's annotationsByArticleIds accepts 1–8 article IDs at a time, in the format “source:ID”, such as MED:14670548 or PMC:4771370, and can be filtered by type (annotation type), section (article section), and provider (annotation provider). annotationsByEntity finds articles by entity name, 1–8 articles per page, and with filter=1 returns only the annotations that match that entity.

https://www.ebi.ac.uk/europepmc/annotations_api/annotationsByArticleIds?articleIds=PMC:4771370&type=Diseases&format=JSON

When this was called on 22 October 2026, the endpoint returned the record for this article (PMID 26864432), but annotations was an empty array. This only shows that the annotation database has no disease annotations for the article; it does not mean the article does not discuss diseases. Removing the type parameter shows which types of annotations the article does have.

Interpreting Results and Limitations

Hit counts are live numbers for a given day. Europe PMC is updated daily, so when reporting search results, state the search date and the complete query. All numbers in this article are results from 22 October 2026.
The same study may have multiple records. The preprint (PPR) and the journal version (MED) are separate records; the 2020 report states that the two are linked to each other. When merging results, deduplicate by DOI and PMID, and decide in advance whether to keep preprints.
Date fields have different meanings. firstIndexDate is the date a record was added to Europe PMC, not the publication date. The first record returned by searching GRANT_AGENCY:"Wellcome Trust" on its own in Example 3 had a firstIndexDate of 2026-09-03 but a pubYear of 2027 (the print issue date comes later). When filtering by time, think carefully about whether to use PUB_YEAR:, FIRST_PDATE:, or FIRST_IDATE:.
A license tag does not mean the full text is readable. The license of that same record shows cc by, but isOpenAccess and inEPMC are both N, and its full-text link is labeled Subscription required. To judge whether an article can be read, first check the availability notes for each link in fullTextUrlList, and then verify with tools such as Unpaywall.
Section searches miss abstract-only articles. When calculating “the proportion of studies using a given method”, use the same full-text scope for both numerator and denominator (for example, add IN_EPMC:y to both); otherwise the proportion will be underestimated.
Field values depend on data entry. Funding agency names and license formats vary, and manual examples may not match the current index (such as GRANT_AGENCY:wellcome above). Before running formal searches, retrieve a few records and check the actual values.
Text mining is automated annotation. It may miss terms or label them incorrectly. It is useful for finding leads but should not be used directly as the basis for including or excluding literature.
Subject-heading searching still relies mainly on PubMed. Europe PMC has no standalone MeSH field. For systematic searches, you can use a PubMed MeSH search strategy as the foundation and then use Europe PMC to add preprints, full-text sections, and the funding dimension.

References

Europe PMC in 2020. Nucleic Acids Research, 49(D1): D1507, published 8 January 2021 (PMID 33180112). https://academic.oup.com/nar/article/49/D1/D1507/5976840
Europe PMC in 2017. Nucleic Acids Research (PMCID PMC5753258). https://pmc.ncbi.nlm.nih.gov/articles/PMC5753258/
EMBL-EBI. EBI Europe PMC SOAP Web Service 6.9.0 Reference Guide, Document Version 1.51, 2023-08-31. https://europepmc.org/docs/EBI_Europe_PMC_Web_Service_Reference.pdf
Europe PMC. Annotations API documentation (accessed 2026-10-22). https://europepmc.org/AnnotationsApi
Europe PMC. REST API fields module (accessed 2026-10-22). https://www.ebi.ac.uk/europepmc/webservices/rest/fields?format=json
Europe PMC. REST API search module (examples in this article called on 2026-10-22). https://www.ebi.ac.uk/europepmc/webservices/rest/search
Gateway to Scholarship · A guide for scholars to living in the intelligent era
Compiled and published by the Scholay All-in-One Academic Platform. If you believe any content infringes your rights, please let us know and it will be taken down.
Also published on Enter Scholar, a community for scholars in the intelligent era

Academic Gateway

A Guide to Penn State Statistics Course Notes

A Guide to Penn State Statistics Course Notes

References

Scope and Rules for Asking Questions on Academia Stack Exchange

Scope and Rules for Asking Questions on Academia Stack Exchange

Scope and Questions That Are Not Accepted

Requirements for Asking and Answering

Voting, Reputation, and Closing Mechanisms

Popular Questions, the Roles of Related Sites, and Limitations

References

Europe PMC Field Searching and API Usage

Europe PMC Field Searching and API Usage

Relationship with PubMed and Coverage

Field Search Syntax and Search Queries

REST API and Text-Mining Annotations

Interpreting Results and Limitations

References